PDB Short entry for 2QQM HEADER SIGNALING PROTEIN 26-JUL-07 2QQM TITLE CRYSTAL STRUCTURE OF THE A2B1B2 DOMAINS FROM HUMAN NEUROPILIN-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEUROPILIN-1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CUB 2, F5/8 TYPE C 1, AND F5/8 TYPE C 2 DOMAINS; COMPND 5 SYNONYM: VASCULAR ENDOTHELIAL CELL GROWTH FACTOR 165 RECEPTOR, CD304 COMPND 6 ANTIGEN; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: NRP1, NRP, VEGF165R; SOURCE 6 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 7 EXPRESSION_SYSTEM_COMMON: CABBAGE LOOPER; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS KEYWDS VEGF RECEPTOR, SEMAPHORIN RECEPTOR, CALCIUM-BINDING DOMAIN, KEYWDS 2 ANGIOGENESIS, DEVELOPMENTAL PROTEIN, DIFFERENTIATION, GLYCOPROTEIN, KEYWDS 3 HEPARAN SULFATE, MEMBRANE, NEUROGENESIS, PROTEOGLYCAN, SECRETED, KEYWDS 4 TRANSMEMBRANE, HORMONE, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR B.A.APPLETON,C.WIESMANN REVDAT 7 30-AUG-23 2QQM 1 HETSYN REVDAT 6 29-JUL-20 2QQM 1 COMPND REMARK SEQADV HETNAM REVDAT 6 2 1 LINK SITE ATOM REVDAT 5 25-OCT-17 2QQM 1 REMARK LINK SITE ATOM REVDAT 4 13-JUL-11 2QQM 1 VERSN REVDAT 3 24-FEB-09 2QQM 1 VERSN REVDAT 2 15-JAN-08 2QQM 1 JRNL REVDAT 1 20-NOV-07 2QQM 0 JRNL AUTH B.A.APPLETON,P.WU,J.MALONEY,J.YIN,W.C.LIANG,S.STAWICKI, JRNL AUTH 2 K.MORTARA,K.K.BOWMAN,J.M.ELLIOTT,W.DESMARAIS,J.F.BAZAN, JRNL AUTH 3 A.BAGRI,M.TESSIER-LAVIGNE,A.W.KOCH,Y.WU,R.J.WATTS,C.WIESMANN JRNL TITL STRUCTURAL STUDIES OF NEUROPILIN/ANTIBODY COMPLEXES PROVIDE JRNL TITL 2 INSIGHTS INTO SEMAPHORIN AND VEGF BINDING JRNL REF EMBO J. V. 26 4902 2007 JRNL REFN ISSN 0261-4189 JRNL PMID 17989695 JRNL DOI 10.1038/SJ.EMBOJ.7601906 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 29213 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) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1558 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 25 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.04 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1517 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.73 REMARK 3 BIN R VALUE (WORKING SET) : 0.2420 REMARK 3 BIN FREE R VALUE SET COUNT : 85 REMARK 3 BIN FREE R VALUE : 0.3110 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3456 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 101 REMARK 3 SOLVENT ATOMS : 194 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 30.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.27 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.38000 REMARK 3 B22 (A**2) : -1.22000 REMARK 3 B33 (A**2) : 4.51000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 2.16000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.193 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.179 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.158 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.623 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.937 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3649 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2572 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4933 ; 1.455 ; 1.981 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6204 ; 0.843 ; 3.003 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 435 ; 6.631 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 161 ;33.335 ;23.727 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 611 ;13.546 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;18.699 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 532 ; 0.083 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3949 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 737 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 644 ; 0.185 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2684 ; 0.195 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1760 ; 0.179 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1957 ; 0.096 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 178 ; 0.156 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 6 ; 0.105 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 12 ; 0.234 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 47 ; 0.213 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 4 ; 0.126 ; 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): 2250 ; 3.511 ; 2.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 889 ; 0.843 ; 2.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3507 ; 4.666 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1643 ; 3.314 ; 2.500 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1425 ; 4.572 ; 5.000 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 : 4 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 145 A 270 REMARK 3 RESIDUE RANGE : A 601 A 601 REMARK 3 RESIDUE RANGE : A 608 A 611 REMARK 3 RESIDUE RANGE : A 612 A 613 REMARK 3 ORIGIN FOR THE GROUP (A): -10.7266 7.3883 14.6973 REMARK 3 T TENSOR REMARK 3 T11: -0.0460 T22: -0.0285 REMARK 3 T33: -0.0869 T12: 0.0100 REMARK 3 T13: 0.0187 T23: 0.0450 REMARK 3 L TENSOR REMARK 3 L11: 2.6741 L22: 1.2902 REMARK 3 L33: 0.6469 L12: 0.0045 REMARK 3 L13: 0.2852 L23: 0.1502 REMARK 3 S TENSOR REMARK 3 S11: -0.0097 S12: 0.0041 S13: 0.0744 REMARK 3 S21: 0.0125 S22: -0.0600 S23: 0.0613 REMARK 3 S31: -0.0417 S32: 0.0361 S33: 0.0697 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 273 A 425 REMARK 3 ORIGIN FOR THE GROUP (A): 3.4981 1.5748 43.1430 REMARK 3 T TENSOR REMARK 3 T11: -0.0115 T22: -0.0334 REMARK 3 T33: -0.0593 T12: 0.0161 REMARK 3 T13: 0.0105 T23: -0.0205 REMARK 3 L TENSOR REMARK 3 L11: 0.7462 L22: 1.0958 REMARK 3 L33: 1.4921 L12: 0.4045 REMARK 3 L13: -0.0058 L23: 0.0301 REMARK 3 S TENSOR REMARK 3 S11: 0.0023 S12: 0.0211 S13: 0.0543 REMARK 3 S21: 0.0686 S22: -0.0128 S23: 0.1945 REMARK 3 S31: -0.0696 S32: -0.0964 S33: 0.0105 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 426 A 586 REMARK 3 ORIGIN FOR THE GROUP (A): 13.5363 -13.1581 14.8863 REMARK 3 T TENSOR REMARK 3 T11: -0.0152 T22: -0.0020 REMARK 3 T33: -0.1897 T12: -0.0095 REMARK 3 T13: -0.0442 T23: -0.0097 REMARK 3 L TENSOR REMARK 3 L11: 1.9166 L22: 3.1716 REMARK 3 L33: 0.6883 L12: -0.0100 REMARK 3 L13: -0.4567 L23: -0.5414 REMARK 3 S TENSOR REMARK 3 S11: -0.0233 S12: 0.0449 S13: -0.1335 REMARK 3 S21: -0.0517 S22: 0.0169 S23: 0.0234 REMARK 3 S31: 0.0717 S32: -0.0124 S33: 0.0064 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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 2QQM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-AUG-07. REMARK 100 THE DEPOSITION ID IS D_1000043932. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-DEC-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL11-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30901 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.8000 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) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.29900 REMARK 200 R SYM FOR SHELL (I) : 0.32200 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 2QQI (B1B2 DOMAINS), 2QQK (A2 DOMAIN) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES, 12% PEG 20000, PH 6.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 297K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 34.08900 REMARK 290 SMTRY3 2 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 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 GLY A 137 REMARK 465 SER A 138 REMARK 465 HIS A 139 REMARK 465 MET A 140 REMARK 465 PHE A 141 REMARK 465 LYS A 142 REMARK 465 ARG A 143 REMARK 465 GLY A 144 REMARK 465 SER A 198 REMARK 465 ASN A 199 REMARK 465 PRO A 200 REMARK 465 PRO A 201 REMARK 465 GLU A 271 REMARK 465 ASP A 272 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 147 CB CYS A 147 SG -0.107 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 VAL A 220 -51.08 -127.08 REMARK 500 ILE A 253 112.38 69.34 REMARK 500 LYS A 255 -166.49 -119.25 REMARK 500 ASN A 313 -150.37 57.92 REMARK 500 THR A 413 -48.58 81.56 REMARK 500 VAL A 465 -55.31 75.45 REMARK 500 SER A 469 -86.62 -145.82 REMARK 500 LYS A 509 85.83 54.34 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 601 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 195 OE1 REMARK 620 2 ASP A 209 OD1 96.8 REMARK 620 3 ASP A 209 OD2 81.0 53.2 REMARK 620 4 ASP A 250 OD1 103.3 74.1 127.1 REMARK 620 5 ALA A 252 O 92.8 148.7 158.1 74.7 REMARK 620 6 ILE A 253 O 89.1 138.3 87.5 144.3 71.3 REMARK 620 7 HOH A 728 O 172.7 88.2 97.8 83.2 85.6 83.6 REMARK 620 N 1 2 3 4 5 6 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2QQI RELATED DB: PDB REMARK 900 RELATED ID: 2QQJ RELATED DB: PDB REMARK 900 RELATED ID: 2QQK RELATED DB: PDB REMARK 900 RELATED ID: 2QQL RELATED DB: PDB REMARK 900 RELATED ID: 2QQN RELATED DB: PDB REMARK 900 RELATED ID: 2QQO RELATED DB: PDB DBREF 2QQM A 141 586 UNP O14786 NRP1_HUMAN 141 586 SEQADV 2QQM GLY A 137 UNP O14786 EXPRESSION TAG SEQADV 2QQM SER A 138 UNP O14786 EXPRESSION TAG SEQADV 2QQM HIS A 139 UNP O14786 EXPRESSION TAG SEQADV 2QQM MET A 140 UNP O14786 EXPRESSION TAG SEQRES 1 A 450 GLY SER HIS MET PHE LYS ARG GLY PRO GLU CYS SER GLN SEQRES 2 A 450 ASN TYR THR THR PRO SER GLY VAL ILE LYS SER PRO GLY SEQRES 3 A 450 PHE PRO GLU LYS TYR PRO ASN SER LEU GLU CYS THR TYR SEQRES 4 A 450 ILE VAL PHE ALA PRO LYS MET SER GLU ILE ILE LEU GLU SEQRES 5 A 450 PHE GLU SER PHE ASP LEU GLU PRO ASP SER ASN PRO PRO SEQRES 6 A 450 GLY GLY MET PHE CYS ARG TYR ASP ARG LEU GLU ILE TRP SEQRES 7 A 450 ASP GLY PHE PRO ASP VAL GLY PRO HIS ILE GLY ARG TYR SEQRES 8 A 450 CYS GLY GLN LYS THR PRO GLY ARG ILE ARG SER SER SER SEQRES 9 A 450 GLY ILE LEU SER MET VAL PHE TYR THR ASP SER ALA ILE SEQRES 10 A 450 ALA LYS GLU GLY PHE SER ALA ASN TYR SER VAL LEU GLN SEQRES 11 A 450 SER SER VAL SER GLU ASP PHE LYS CYS MET GLU ALA LEU SEQRES 12 A 450 GLY MET GLU SER GLY GLU ILE HIS SER ASP GLN ILE THR SEQRES 13 A 450 ALA SER SER GLN TYR SER THR ASN TRP SER ALA GLU ARG SEQRES 14 A 450 SER ARG LEU ASN TYR PRO GLU ASN GLY TRP THR PRO GLY SEQRES 15 A 450 GLU ASP SER TYR ARG GLU TRP ILE GLN VAL ASP LEU GLY SEQRES 16 A 450 LEU LEU ARG PHE VAL THR ALA VAL GLY THR GLN GLY ALA SEQRES 17 A 450 ILE SER LYS GLU THR LYS LYS LYS TYR TYR VAL LYS THR SEQRES 18 A 450 TYR LYS ILE ASP VAL SER SER ASN GLY GLU ASP TRP ILE SEQRES 19 A 450 THR ILE LYS GLU GLY ASN LYS PRO VAL LEU PHE GLN GLY SEQRES 20 A 450 ASN THR ASN PRO THR ASP VAL VAL VAL ALA VAL PHE PRO SEQRES 21 A 450 LYS PRO LEU ILE THR ARG PHE VAL ARG ILE LYS PRO ALA SEQRES 22 A 450 THR TRP GLU THR GLY ILE SER MET ARG PHE GLU VAL TYR SEQRES 23 A 450 GLY CYS LYS ILE THR ASP TYR PRO CYS SER GLY MET LEU SEQRES 24 A 450 GLY MET VAL SER GLY LEU ILE SER ASP SER GLN ILE THR SEQRES 25 A 450 SER SER ASN GLN GLY ASP ARG ASN TRP MET PRO GLU ASN SEQRES 26 A 450 ILE ARG LEU VAL THR SER ARG SER GLY TRP ALA LEU PRO SEQRES 27 A 450 PRO ALA PRO HIS SER TYR ILE ASN GLU TRP LEU GLN ILE SEQRES 28 A 450 ASP LEU GLY GLU GLU LYS ILE VAL ARG GLY ILE ILE ILE SEQRES 29 A 450 GLN GLY GLY LYS HIS ARG GLU ASN LYS VAL PHE MET ARG SEQRES 30 A 450 LYS PHE LYS ILE GLY TYR SER ASN ASN GLY SER ASP TRP SEQRES 31 A 450 LYS MET ILE MET ASP ASP SER LYS ARG LYS ALA LYS SER SEQRES 32 A 450 PHE GLU GLY ASN ASN ASN TYR ASP THR PRO GLU LEU ARG SEQRES 33 A 450 THR PHE PRO ALA LEU SER THR ARG PHE ILE ARG ILE TYR SEQRES 34 A 450 PRO GLU ARG ALA THR HIS GLY GLY LEU GLY LEU ARG MET SEQRES 35 A 450 GLU LEU LEU GLY CYS GLU VAL GLU MODRES 2QQM ASN A 150 ASN GLYCOSYLATION SITE MODRES 2QQM ASN A 261 ASN GLYCOSYLATION SITE HET NAG B 1 14 HET FUC B 2 10 HET NAG B 3 14 HET FUC B 4 10 HET NAG C 1 14 HET NAG C 2 14 HET CA A 601 1 HET EDO A 602 4 HET EDO A 603 4 HET EDO A 604 4 HET EDO A 605 4 HET EDO A 606 4 HET EDO A 607 4 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE HETNAM CA CALCIUM ION HETNAM EDO 1,2-ETHANEDIOL 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 FUC ALPHA-L-FUCOSE; 6-DEOXY-ALPHA-L-GALACTOPYRANOSE; L- HETSYN 2 FUC FUCOSE; FUCOSE HETSYN EDO ETHYLENE GLYCOL FORMUL 2 NAG 4(C8 H15 N O6) FORMUL 2 FUC 2(C6 H12 O5) FORMUL 4 CA CA 2+ FORMUL 5 EDO 6(C2 H6 O2) FORMUL 11 HOH *194(H2 O) HELIX 1 1 PRO A 180 SER A 183 5 4 HELIX 2 2 HIS A 287 ASP A 289 5 3 HELIX 3 3 SER A 298 ARG A 307 5 10 HELIX 4 4 LYS A 425 TYR A 429 5 5 HELIX 5 5 SER A 443 SER A 445 5 3 HELIX 6 6 MET A 458 ARG A 463 5 6 SHEET 1 A 5 GLN A 149 TYR A 151 0 SHEET 2 A 5 GLU A 172 PHE A 178 1 O PHE A 178 N TYR A 151 SHEET 3 A 5 ILE A 242 TYR A 248 -1 O LEU A 243 N VAL A 177 SHEET 4 A 5 ARG A 210 TRP A 214 -1 N ARG A 210 O TYR A 248 SHEET 5 A 5 HIS A 223 TYR A 227 -1 O ILE A 224 N ILE A 213 SHEET 1 B 4 SER A 155 LYS A 159 0 SHEET 2 B 4 GLY A 257 VAL A 264 -1 O ALA A 260 N ILE A 158 SHEET 3 B 4 ILE A 185 ASP A 193 -1 N ILE A 186 O SER A 263 SHEET 4 B 4 ARG A 235 SER A 238 -1 O ILE A 236 N LEU A 187 SHEET 1 C 9 ILE A 291 ALA A 293 0 SHEET 2 C 9 ILE A 326 GLN A 342 -1 O GLN A 327 N THR A 292 SHEET 3 C 9 VAL A 391 GLU A 412 -1 O ILE A 406 N ILE A 326 SHEET 4 C 9 LYS A 352 SER A 363 -1 N ASP A 361 O ARG A 405 SHEET 5 C 9 ALA A 344 ILE A 345 -1 N ALA A 344 O TYR A 353 SHEET 6 C 9 LYS A 352 SER A 363 -1 O TYR A 353 N ALA A 344 SHEET 7 C 9 TRP A 369 THR A 371 -1 O ILE A 370 N VAL A 362 SHEET 8 C 9 LYS A 352 SER A 363 -1 N VAL A 362 O ILE A 370 SHEET 9 C 9 PHE A 381 GLN A 382 -1 O PHE A 381 N TYR A 358 SHEET 1 D 3 ILE A 326 GLN A 342 0 SHEET 2 D 3 ARG A 418 CYS A 424 -1 O ARG A 418 N GLN A 342 SHEET 3 D 3 GLU A 277 ALA A 278 -1 N GLU A 277 O GLY A 423 SHEET 1 E12 GLY A 433 MET A 434 0 SHEET 2 E12 LEU A 574 CYS A 583 -1 O GLY A 582 N GLY A 433 SHEET 3 E12 TRP A 471 LEU A 473 -1 N TRP A 471 O LEU A 576 SHEET 4 E12 LEU A 574 CYS A 583 -1 O LEU A 576 N TRP A 471 SHEET 5 E12 LEU A 485 GLN A 501 -1 N ILE A 494 O CYS A 583 SHEET 6 E12 ILE A 447 SER A 449 -1 N THR A 448 O GLN A 486 SHEET 7 E12 LEU A 485 GLN A 501 -1 O GLN A 486 N THR A 448 SHEET 8 E12 GLU A 550 ALA A 569 -1 O ILE A 562 N ILE A 487 SHEET 9 E12 MET A 512 SER A 520 -1 N ARG A 513 O ARG A 568 SHEET 10 E12 PHE A 540 GLU A 541 -1 O PHE A 540 N PHE A 515 SHEET 11 E12 MET A 512 SER A 520 -1 N PHE A 515 O PHE A 540 SHEET 12 E12 LYS A 527 MET A 528 -1 O LYS A 527 N TYR A 519 SSBOND 1 CYS A 147 CYS A 173 1555 1555 2.03 SSBOND 2 CYS A 206 CYS A 228 1555 1555 2.07 SSBOND 3 CYS A 275 CYS A 424 1555 1555 2.07 SSBOND 4 CYS A 431 CYS A 583 1555 1555 2.07 LINK ND2 ASN A 150 C1 NAG C 1 1555 1555 1.45 LINK ND2 ASN A 261 C1 NAG B 1 1555 1555 1.46 LINK O3 NAG B 1 C1 FUC B 2 1555 1555 1.45 LINK O4 NAG B 1 C1 NAG B 3 1555 1555 1.45 LINK O6 NAG B 1 C1 FUC B 4 1555 1555 1.45 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.45 LINK OE1 GLU A 195 CA CA A 601 1555 1555 2.25 LINK OD1 ASP A 209 CA CA A 601 1555 1555 2.47 LINK OD2 ASP A 209 CA CA A 601 1555 1555 2.40 LINK OD1 ASP A 250 CA CA A 601 1555 1555 2.30 LINK O ALA A 252 CA CA A 601 1555 1555 2.31 LINK O ILE A 253 CA CA A 601 1555 1555 2.32 LINK CA CA A 601 O HOH A 728 1555 1555 2.42 CISPEP 1 PHE A 163 PRO A 164 0 1.78 CRYST1 53.177 68.178 66.613 90.00 102.10 90.00 P 1 21 1 2 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 0.018805 0.000000 0.004032 0.00000 SCALE2 0.000000 0.014667 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015353 0.00000