PDB Short entry for 3F6K HEADER SIGNALING PROTEIN 06-NOV-08 3F6K TITLE CRYSTAL STRUCTURE OF THE VPS10P DOMAIN OF HUMAN SORTILIN/NTS3 IN TITLE 2 COMPLEX WITH NEUROTENSIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SORTILIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 78-756; COMPND 5 SYNONYM: NEUROTENSIN RECEPTOR 3, NTR3, NTS3, GLYCOPROTEIN 95, GP95, COMPND 6 100 KDA NT RECEPTOR; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: NEUROTENSIN; COMPND 10 CHAIN: N; COMPND 11 FRAGMENT: UNP RESIDUES 151-163; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 GENE: SORT1; SOURCE 5 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: CHO-K1; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 OTHER_DETAILS: SYNTHETIC PEPTIDE PURCHASED FROM SIGMA. IT REPRESENTS SOURCE 11 THE NATURALLY OCCURRING FORM OF NEUROTENSIN IN HUMAN, RESIDUES 151- SOURCE 12 163 OF UNIPROT ENTRY P30990, NEUT_HUMAN KEYWDS PROTEIN SORTING RECEPTOR, 10-BLADED BETA-PROPELLER, CYS-RICH DOMAINS, KEYWDS 2 SSORTILIN, SORTILIN VPS10P-D, PROTEIN-PEPTIDE COMPLEX, DEVELOPMENTAL KEYWDS 3 PROTEIN, DIFFERENTIATION, ENDOCYTOSIS, ENDOPLASMIC RETICULUM, KEYWDS 4 ENDOSOME, GLYCOPROTEIN, GOLGI APPARATUS, LYSOSOME, MEMBRANE, KEYWDS 5 PHOSPHOPROTEIN, RECEPTOR, TRANSMEMBRANE, TRANSPORT, CYTOPLASMIC KEYWDS 6 VESICLE, SECRETED, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR E.M.QUISTGAARD,P.MADSEN,M.K.GROFTEHAUGE,P.NISSEN,C.M.PETERSEN, AUTHOR 2 S.THIRUP REVDAT 6 27-DEC-23 3F6K 1 HETSYN REVDAT 5 29-JUL-20 3F6K 1 COMPND REMARK HETNAM LINK REVDAT 5 2 1 SITE ATOM REVDAT 4 25-DEC-19 3F6K 1 SEQADV SEQRES LINK REVDAT 3 13-JUL-11 3F6K 1 VERSN REVDAT 2 27-JAN-09 3F6K 1 JRNL REVDAT 1 30-DEC-08 3F6K 0 JRNL AUTH E.M.QUISTGAARD,P.MADSEN,M.K.GROFTEHAUGE,P.NISSEN, JRNL AUTH 2 C.M.PETERSEN,S.S.THIRUP JRNL TITL LIGANDS BIND TO SORTILIN IN THE TUNNEL OF A TEN-BLADED JRNL TITL 2 BETA-PROPELLER DOMAIN. JRNL REF NAT.STRUCT.MOL.BIOL. V. 16 96 2009 JRNL REFN ISSN 1545-9993 JRNL PMID 19122660 JRNL DOI 10.1038/NSMB.1543 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.32 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 56985 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2904 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4048 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.12 REMARK 3 BIN R VALUE (WORKING SET) : 0.2240 REMARK 3 BIN FREE R VALUE SET COUNT : 218 REMARK 3 BIN FREE R VALUE : 0.2570 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5212 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 83 REMARK 3 SOLVENT ATOMS : 305 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 37.05 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.78 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.58000 REMARK 3 B22 (A**2) : 1.22000 REMARK 3 B33 (A**2) : -1.67000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.78000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.176 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.151 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.110 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.610 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.941 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5428 ; 0.021 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7357 ; 1.832 ; 1.960 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 658 ; 7.053 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 250 ;35.684 ;24.160 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 890 ;16.770 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;22.079 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 808 ; 0.137 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4092 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2229 ; 0.238 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3763 ; 0.319 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 372 ; 0.268 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 54 ; 0.223 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 13 ; 0.235 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 3359 ; 1.446 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5288 ; 2.290 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2370 ; 3.273 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2069 ; 4.816 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 55 A 155 REMARK 3 ORIGIN FOR THE GROUP (A): 42.8376 69.7777 16.9772 REMARK 3 T TENSOR REMARK 3 T11: 0.1094 T22: 0.1567 REMARK 3 T33: 0.0902 T12: -0.0988 REMARK 3 T13: -0.0413 T23: 0.0524 REMARK 3 L TENSOR REMARK 3 L11: 2.1236 L22: 6.5272 REMARK 3 L33: 1.8762 L12: -1.2281 REMARK 3 L13: -0.3690 L23: 0.6749 REMARK 3 S TENSOR REMARK 3 S11: 0.0369 S12: -0.1308 S13: 0.2061 REMARK 3 S21: 0.6073 S22: -0.0793 S23: -0.4944 REMARK 3 S31: -0.0819 S32: 0.3481 S33: 0.0424 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 156 A 629 REMARK 3 ORIGIN FOR THE GROUP (A): 20.6468 66.7618 21.8714 REMARK 3 T TENSOR REMARK 3 T11: 0.0200 T22: 0.0179 REMARK 3 T33: -0.0272 T12: -0.0026 REMARK 3 T13: 0.0013 T23: 0.0147 REMARK 3 L TENSOR REMARK 3 L11: 1.0707 L22: 0.6614 REMARK 3 L33: 0.9161 L12: -0.0319 REMARK 3 L13: -0.0732 L23: 0.1245 REMARK 3 S TENSOR REMARK 3 S11: 0.0047 S12: -0.1525 S13: 0.1061 REMARK 3 S21: 0.0768 S22: -0.0297 S23: -0.0546 REMARK 3 S31: -0.1289 S32: 0.0460 S33: 0.0250 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 630 A 716 REMARK 3 ORIGIN FOR THE GROUP (A): -11.1651 73.6956 23.9775 REMARK 3 T TENSOR REMARK 3 T11: 0.1541 T22: 0.2974 REMARK 3 T33: 0.1577 T12: 0.0515 REMARK 3 T13: 0.0235 T23: -0.1171 REMARK 3 L TENSOR REMARK 3 L11: 0.7834 L22: 3.4911 REMARK 3 L33: 6.5078 L12: -1.4728 REMARK 3 L13: -2.2280 L23: 4.5405 REMARK 3 S TENSOR REMARK 3 S11: -0.1039 S12: 0.0673 S13: -0.0532 REMARK 3 S21: 0.2652 S22: -0.4227 S23: 0.4413 REMARK 3 S31: 0.1682 S32: -0.6475 S33: 0.5266 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3F6K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-NOV-08. REMARK 100 THE DEPOSITION ID IS D_1000050209. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-OCT-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.95008 REMARK 200 MONOCHROMATOR : FIXED-EXIT LN2 COOLED DOUBLE REMARK 200 CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS, XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 56985 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.5900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.44000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.320 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIRAS REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 19% PEG 6000, 600 MM NACL, 3% REMARK 280 GLYCEROL, 100 MM HEPES, 93 MM TRIS-HCL, PH 7.8, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 72.88000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.26500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 72.88000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 37.26500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 REMARK: THE BIOLOGICAL UNIT IS A HETERODIMERIC COMPLEX OF THE REMARK 300 PROTEIN MONOMER WITH THE PEPTIDE MONOMER. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 830 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30600 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.6 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, N, B, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A1280 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 AUTHORS STATE THAT THE GLYCOSYLATIONS ARE COVALENTLY REMARK 400 ATTACHED TO THE ASPARAGINES, THEREFORE THEY SHOULD NOT BE REMARK 400 DESCRIBED AS SITE RECORDS. INSTEAD, WHAT SHOULD BE SHOWN REMARK 400 IN SITE RECORDS, IS THE NEUROTENSIN BINDING SITE. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 SER A 45 REMARK 465 ALA A 46 REMARK 465 PRO A 47 REMARK 465 GLY A 48 REMARK 465 GLU A 49 REMARK 465 ASP A 50 REMARK 465 GLU A 51 REMARK 465 GLU A 52 REMARK 465 CYS A 53 REMARK 465 GLY A 54 REMARK 465 VAL A 102 REMARK 465 ILE A 103 REMARK 465 MET A 104 REMARK 465 THR A 105 REMARK 465 PHE A 106 REMARK 465 GLN A 717 REMARK 465 ASN A 718 REMARK 465 SER A 719 REMARK 465 LYS A 720 REMARK 465 SER A 721 REMARK 465 ASN A 722 REMARK 465 SER A 723 REMARK 465 HIS A 724 REMARK 465 HIS A 725 REMARK 465 HIS A 726 REMARK 465 HIS A 727 REMARK 465 HIS A 728 REMARK 465 HIS A 729 REMARK 465 PCA N 1 REMARK 465 LEU N 2 REMARK 465 TYR N 3 REMARK 465 GLU N 4 REMARK 465 ASN N 5 REMARK 465 LYS N 6 REMARK 465 PRO N 7 REMARK 465 ARG N 8 REMARK 465 ARG N 9 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 1069 O HOH A 1270 2.13 REMARK 500 OE1 GLU A 607 O HOH A 1270 2.18 REMARK 500 O HOH A 1102 O HOH A 1272 2.18 REMARK 500 O HOH A 1151 O HOH A 1215 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 CYS A 224 CB CYS A 224 SG -0.110 REMARK 500 GLU A 487 CG GLU A 487 CD 0.110 REMARK 500 ARG A 698 CZ ARG A 698 NH1 0.078 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 293 CB - CA - C ANGL. DEV. = -14.0 DEGREES REMARK 500 ARG A 293 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ASP A 570 CB - CG - OD1 ANGL. DEV. = 6.0 DEGREES REMARK 500 ARG A 698 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LEU A 75 37.87 -154.61 REMARK 500 GLU A 144 -134.37 50.33 REMARK 500 ASN A 241 -72.53 164.14 REMARK 500 SER A 243 149.04 14.19 REMARK 500 ASN A 324 -158.31 -137.54 REMARK 500 ASP A 337 75.93 21.03 REMARK 500 ASP A 347 -171.04 -67.09 REMARK 500 ASP A 399 51.95 -118.85 REMARK 500 ASP A 416 -168.67 -77.57 REMARK 500 CYS A 425 -165.91 -163.03 REMARK 500 ALA A 431 -143.65 -140.84 REMARK 500 ASP A 496 60.38 32.19 REMARK 500 ASN A 512 21.13 -149.42 REMARK 500 GLN A 563 143.43 -172.44 REMARK 500 GLU A 650 -63.19 -14.04 REMARK 500 ASN A 651 -146.20 -113.23 REMARK 500 SER A 653 28.70 99.69 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ASP A 652 SER A 653 142.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 999 REMARK 999 SEQUENCE REMARK 999 IN VIVO, NEUROTENSIN (ENTITY 2) IS PRODUCED BY PROTEOLYTIC REMARK 999 CLEAVAGE OF THE GENE PRODUCT, AND THE RESULTING N-TERMINAL REMARK 999 GLUTAMATE IS NATURALLY CONVERTED TO PYROGLUTAMATE. DBREF 3F6K A 45 723 UNP Q99523 SORT_HUMAN 78 756 DBREF 3F6K N 1 13 UNP P30990 NEUT_HUMAN 151 163 SEQADV 3F6K MET A 617 UNP Q99523 VAL 650 VARIANT SEQADV 3F6K HIS A 724 UNP Q99523 EXPRESSION TAG SEQADV 3F6K HIS A 725 UNP Q99523 EXPRESSION TAG SEQADV 3F6K HIS A 726 UNP Q99523 EXPRESSION TAG SEQADV 3F6K HIS A 727 UNP Q99523 EXPRESSION TAG SEQADV 3F6K HIS A 728 UNP Q99523 EXPRESSION TAG SEQADV 3F6K HIS A 729 UNP Q99523 EXPRESSION TAG SEQRES 1 A 685 SER ALA PRO GLY GLU ASP GLU GLU CYS GLY ARG VAL ARG SEQRES 2 A 685 ASP PHE VAL ALA LYS LEU ALA ASN ASN THR HIS GLN HIS SEQRES 3 A 685 VAL PHE ASP ASP LEU ARG GLY SER VAL SER LEU SER TRP SEQRES 4 A 685 VAL GLY ASP SER THR GLY VAL ILE LEU VAL LEU THR THR SEQRES 5 A 685 PHE HIS VAL PRO LEU VAL ILE MET THR PHE GLY GLN SER SEQRES 6 A 685 LYS LEU TYR ARG SER GLU ASP TYR GLY LYS ASN PHE LYS SEQRES 7 A 685 ASP ILE THR ASP LEU ILE ASN ASN THR PHE ILE ARG THR SEQRES 8 A 685 GLU PHE GLY MET ALA ILE GLY PRO GLU ASN SER GLY LYS SEQRES 9 A 685 VAL VAL LEU THR ALA GLU VAL SER GLY GLY SER ARG GLY SEQRES 10 A 685 GLY ARG ILE PHE ARG SER SER ASP PHE ALA LYS ASN PHE SEQRES 11 A 685 VAL GLN THR ASP LEU PRO PHE HIS PRO LEU THR GLN MET SEQRES 12 A 685 MET TYR SER PRO GLN ASN SER ASP TYR LEU LEU ALA LEU SEQRES 13 A 685 SER THR GLU ASN GLY LEU TRP VAL SER LYS ASN PHE GLY SEQRES 14 A 685 GLY LYS TRP GLU GLU ILE HIS LYS ALA VAL CYS LEU ALA SEQRES 15 A 685 LYS TRP GLY SER ASP ASN THR ILE PHE PHE THR THR TYR SEQRES 16 A 685 ALA ASN GLY SER CYS LYS ALA ASP LEU GLY ALA LEU GLU SEQRES 17 A 685 LEU TRP ARG THR SER ASP LEU GLY LYS SER PHE LYS THR SEQRES 18 A 685 ILE GLY VAL LYS ILE TYR SER PHE GLY LEU GLY GLY ARG SEQRES 19 A 685 PHE LEU PHE ALA SER VAL MET ALA ASP LYS ASP THR THR SEQRES 20 A 685 ARG ARG ILE HIS VAL SER THR ASP GLN GLY ASP THR TRP SEQRES 21 A 685 SER MET ALA GLN LEU PRO SER VAL GLY GLN GLU GLN PHE SEQRES 22 A 685 TYR SER ILE LEU ALA ALA ASN ASP ASP MET VAL PHE MET SEQRES 23 A 685 HIS VAL ASP GLU PRO GLY ASP THR GLY PHE GLY THR ILE SEQRES 24 A 685 PHE THR SER ASP ASP ARG GLY ILE VAL TYR SER LYS SER SEQRES 25 A 685 LEU ASP ARG HIS LEU TYR THR THR THR GLY GLY GLU THR SEQRES 26 A 685 ASP PHE THR ASN VAL THR SER LEU ARG GLY VAL TYR ILE SEQRES 27 A 685 THR SER VAL LEU SER GLU ASP ASN SER ILE GLN THR MET SEQRES 28 A 685 ILE THR PHE ASP GLN GLY GLY ARG TRP THR HIS LEU ARG SEQRES 29 A 685 LYS PRO GLU ASN SER GLU CYS ASP ALA THR ALA LYS ASN SEQRES 30 A 685 LYS ASN GLU CYS SER LEU HIS ILE HIS ALA SER TYR SER SEQRES 31 A 685 ILE SER GLN LYS LEU ASN VAL PRO MET ALA PRO LEU SER SEQRES 32 A 685 GLU PRO ASN ALA VAL GLY ILE VAL ILE ALA HIS GLY SER SEQRES 33 A 685 VAL GLY ASP ALA ILE SER VAL MET VAL PRO ASP VAL TYR SEQRES 34 A 685 ILE SER ASP ASP GLY GLY TYR SER TRP THR LYS MET LEU SEQRES 35 A 685 GLU GLY PRO HIS TYR TYR THR ILE LEU ASP SER GLY GLY SEQRES 36 A 685 ILE ILE VAL ALA ILE GLU HIS SER SER ARG PRO ILE ASN SEQRES 37 A 685 VAL ILE LYS PHE SER THR ASP GLU GLY GLN CYS TRP GLN SEQRES 38 A 685 THR TYR THR PHE THR ARG ASP PRO ILE TYR PHE THR GLY SEQRES 39 A 685 LEU ALA SER GLU PRO GLY ALA ARG SER MET ASN ILE SER SEQRES 40 A 685 ILE TRP GLY PHE THR GLU SER PHE LEU THR SER GLN TRP SEQRES 41 A 685 VAL SER TYR THR ILE ASP PHE LYS ASP ILE LEU GLU ARG SEQRES 42 A 685 ASN CYS GLU GLU LYS ASP TYR THR ILE TRP LEU ALA HIS SEQRES 43 A 685 SER THR ASP PRO GLU ASP TYR GLU ASP GLY CYS ILE LEU SEQRES 44 A 685 GLY TYR LYS GLU GLN PHE LEU ARG LEU ARG LYS SER SER SEQRES 45 A 685 MET CYS GLN ASN GLY ARG ASP TYR VAL VAL THR LYS GLN SEQRES 46 A 685 PRO SER ILE CYS LEU CYS SER LEU GLU ASP PHE LEU CYS SEQRES 47 A 685 ASP PHE GLY TYR TYR ARG PRO GLU ASN ASP SER LYS CYS SEQRES 48 A 685 VAL GLU GLN PRO GLU LEU LYS GLY HIS ASP LEU GLU PHE SEQRES 49 A 685 CYS LEU TYR GLY ARG GLU GLU HIS LEU THR THR ASN GLY SEQRES 50 A 685 TYR ARG LYS ILE PRO GLY ASP LYS CYS GLN GLY GLY VAL SEQRES 51 A 685 ASN PRO VAL ARG GLU VAL LYS ASP LEU LYS LYS LYS CYS SEQRES 52 A 685 THR SER ASN PHE LEU SER PRO GLU LYS GLN ASN SER LYS SEQRES 53 A 685 SER ASN SER HIS HIS HIS HIS HIS HIS SEQRES 1 N 13 PCA LEU TYR GLU ASN LYS PRO ARG ARG PRO TYR ILE LEU MODRES 3F6K ASN A 373 ASN GLYCOSYLATION SITE MODRES 3F6K ASN A 549 ASN GLYCOSYLATION SITE HET NAG B 1 14 HET NAG B 2 14 HET NAG C 1 14 HET NAG C 2 14 HET BMA C 3 11 HET PGE A 951 10 HET GOL A 952 6 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM PGE TRIETHYLENE GLYCOL HETNAM GOL GLYCEROL HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 NAG 4(C8 H15 N O6) FORMUL 4 BMA C6 H12 O6 FORMUL 5 PGE C6 H14 O4 FORMUL 6 GOL C3 H8 O3 FORMUL 7 HOH *305(H2 O) HELIX 1 1 ASP A 58 ASN A 65 1 8 HELIX 2 2 THR A 125 ASN A 129 5 5 HELIX 3 3 ARG A 134 PHE A 137 5 4 HELIX 4 4 ALA A 431 GLN A 437 1 7 HELIX 5 5 ASP A 496 GLY A 499 5 4 HELIX 6 6 LYS A 572 ILE A 574 5 3 HELIX 7 7 GLU A 580 LYS A 582 5 3 HELIX 8 8 SER A 636 GLU A 638 5 3 HELIX 9 9 LYS A 662 GLY A 672 1 11 HELIX 10 10 ARG A 673 LEU A 677 1 5 HELIX 11 11 LEU A 703 THR A 708 1 6 HELIX 12 12 SER A 709 PHE A 711 5 3 SHEET 1 A 4 THR A 67 PHE A 72 0 SHEET 2 A 4 SER A 562 ASP A 570 -1 O THR A 568 N HIS A 68 SHEET 3 A 4 ASN A 549 GLU A 557 -1 N ILE A 552 O TYR A 567 SHEET 4 A 4 TYR A 535 ALA A 540 -1 N GLY A 538 O TRP A 553 SHEET 1 B 4 SER A 78 TRP A 83 0 SHEET 2 B 4 ILE A 91 PHE A 97 -1 O LEU A 94 N SER A 80 SHEET 3 B 4 GLN A 108 SER A 114 -1 O TYR A 112 N VAL A 93 SHEET 4 B 4 LYS A 122 ASP A 123 -1 O LYS A 122 N ARG A 113 SHEET 1 C 4 MET A 139 ILE A 141 0 SHEET 2 C 4 VAL A 149 ALA A 153 -1 O VAL A 150 N ALA A 140 SHEET 3 C 4 ARG A 163 SER A 167 -1 O ARG A 163 N ALA A 153 SHEET 4 C 4 VAL A 175 ASP A 178 -1 O THR A 177 N ILE A 164 SHEET 1 D 4 MET A 188 SER A 190 0 SHEET 2 D 4 ASN A 193 LEU A 200 -1 O TYR A 196 N SER A 190 SHEET 3 D 4 LEU A 206 SER A 209 -1 O TRP A 207 N ALA A 199 SHEET 4 D 4 TRP A 216 HIS A 220 -1 O HIS A 220 N LEU A 206 SHEET 1 E 7 VAL A 223 TRP A 228 0 SHEET 2 E 7 ILE A 234 THR A 238 -1 O PHE A 235 N LYS A 227 SHEET 3 E 7 LEU A 251 THR A 256 -1 O TRP A 254 N PHE A 236 SHEET 4 E 7 LYS A 264 GLY A 276 -1 O LYS A 264 N ARG A 255 SHEET 5 E 7 PHE A 279 MET A 285 -1 O PHE A 281 N GLY A 274 SHEET 6 E 7 ARG A 292 SER A 297 -1 O ARG A 293 N VAL A 284 SHEET 7 E 7 SER A 305 MET A 306 -1 O SER A 305 N VAL A 296 SHEET 1 F 5 TYR A 353 LEU A 361 0 SHEET 2 F 5 PHE A 340 SER A 346 -1 N ILE A 343 O SER A 356 SHEET 3 F 5 VAL A 328 ASP A 333 -1 N MET A 330 O PHE A 344 SHEET 4 F 5 TYR A 318 ALA A 323 -1 N SER A 319 O HIS A 331 SHEET 5 F 5 TYR N 11 ILE N 12 -1 O TYR N 11 N ILE A 320 SHEET 1 G 8 THR A 372 ASN A 373 0 SHEET 2 G 8 TYR A 381 LEU A 386 -1 O ILE A 382 N THR A 372 SHEET 3 G 8 ILE A 392 THR A 397 -1 O GLN A 393 N VAL A 385 SHEET 4 G 8 THR A 405 ARG A 408 -1 O THR A 405 N ILE A 396 SHEET 5 G 8 SER A 426 ILE A 429 -1 O LEU A 427 N LEU A 407 SHEET 6 G 8 VAL A 455 GLY A 462 -1 O GLY A 462 N SER A 426 SHEET 7 G 8 ASP A 471 SER A 475 -1 O TYR A 473 N ALA A 457 SHEET 8 G 8 THR A 483 LEU A 486 -1 O MET A 485 N VAL A 472 SHEET 1 H 4 HIS A 490 LEU A 495 0 SHEET 2 H 4 ILE A 500 GLU A 505 -1 O ILE A 500 N LEU A 495 SHEET 3 H 4 VAL A 513 SER A 517 -1 O LYS A 515 N ALA A 503 SHEET 4 H 4 GLN A 525 THR A 528 -1 O TYR A 527 N ILE A 514 SHEET 1 I 3 TYR A 584 LEU A 588 0 SHEET 2 I 3 TYR A 605 LEU A 612 -1 O PHE A 609 N TRP A 587 SHEET 3 I 3 LYS A 628 ILE A 632 -1 O SER A 631 N LYS A 606 SHEET 1 J 2 PHE A 640 CYS A 642 0 SHEET 2 J 2 TYR A 682 LYS A 684 -1 O ARG A 683 N LEU A 641 SHEET 1 K 2 TYR A 646 TYR A 647 0 SHEET 2 K 2 VAL A 656 GLU A 657 -1 O VAL A 656 N TYR A 647 SHEET 1 L 2 THR A 678 THR A 679 0 SHEET 2 L 2 LYS A 701 ASP A 702 -1 O LYS A 701 N THR A 679 SSBOND 1 CYS A 224 CYS A 244 1555 1555 2.08 SSBOND 2 CYS A 415 CYS A 425 1555 1555 2.08 SSBOND 3 CYS A 579 CYS A 618 1555 1555 2.15 SSBOND 4 CYS A 601 CYS A 633 1555 1555 2.05 SSBOND 5 CYS A 635 CYS A 690 1555 1555 2.12 SSBOND 6 CYS A 642 CYS A 655 1555 1555 2.07 SSBOND 7 CYS A 669 CYS A 707 1555 1555 2.74 LINK ND2 ASN A 373 C1 NAG B 1 1555 1555 1.46 LINK ND2 ASN A 549 C1 NAG C 1 1555 1555 1.45 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.45 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.44 LINK O4 NAG C 2 C1 BMA C 3 1555 1555 1.47 CRYST1 145.760 74.530 108.330 90.00 131.87 90.00 C 1 2 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.006861 0.000000 0.006149 0.00000 SCALE2 0.000000 0.013417 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012396 0.00000