PDB Short entry for 1F8P HEADER NEUROPEPTIDE 03-JUL-00 1F8P TITLE PORCINE NEUROPEPTIDE Y BOUND TO DPC MICELLES COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEUROPEPTIDE Y (PNPY); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: CHEMICALLY SYNTHESIZED SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: OCCURS IN NERVOUS SYSTEM OF PIGS KEYWDS HELIX, NEUROPEPTIDE EXPDTA SOLUTION NMR NUMMDL 17 AUTHOR R.BADER,A.G.BECK-SICKINGER,O.ZERBE REVDAT 3 23-FEB-22 1F8P 1 REMARK LINK REVDAT 2 24-FEB-09 1F8P 1 VERSN REVDAT 1 03-JAN-01 1F8P 0 JRNL AUTH R.BADER,A.BETTIO,A.G.BECK-SICKINGER,O.ZERBE JRNL TITL STRUCTURE AND DYNAMICS OF MICELLE-BOUND NEUROPEPTIDE Y: JRNL TITL 2 COMPARISON WITH UNLIGATED NPY AND IMPLICATIONS FOR RECEPTOR JRNL TITL 3 SELECTION. JRNL REF J.MOL.BIOL. V. 305 307 2001 JRNL REFN ISSN 0022-2836 JRNL PMID 11124908 JRNL DOI 10.1006/JMBI.2000.4264 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.1, AMBER 4.1 REMARK 3 AUTHORS : BRUKER (XWINNMR), KOLLMAN (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 344 NOE-BASED DISTANCE RESTRAINTS 145 REMARK 3 DIHEDRAL ANGLE CONSTRAINTS REMARK 4 REMARK 4 1F8P COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JUL-00. REMARK 100 THE DEPOSITION ID IS D_1000011380. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 3MM PNPY, 300MM D-38 DPC; 3MM REMARK 210 PNPY, 300MM D-38 DPC REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; E-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XEASY 1.3.13, DYANA 1.5 REMARK 210 METHOD USED : SIMMULATED ANNEALING IN TORSION REMARK 210 ANGLE SPACE REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 17 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY,STRUCTURES REMARK 210 WITH FAVORABLE NON-BOND ENERGY, REMARK 210 STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS,STRUCTURES REMARK 210 WITH THE LOWEST ENERGY,TARGET REMARK 210 FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: 75 MS NOESY REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 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 15 GLU A 10 CD GLU A 10 OE2 -0.074 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 7 ASP A 16 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 12 ASP A 6 CB - CG - OD2 ANGL. DEV. = -7.6 DEGREES REMARK 500 13 TYR A 36 CB - CG - CD2 ANGL. DEV. = -3.9 DEGREES REMARK 500 15 ASP A 16 CB - CG - OD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 16 TYR A 21 CB - CG - CD1 ANGL. DEV. = -3.8 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 1 ASP A 11 94.06 -177.00 REMARK 500 1 ALA A 12 156.09 -49.35 REMARK 500 1 TYR A 27 -74.07 -67.73 REMARK 500 2 SER A 3 -56.81 -155.29 REMARK 500 2 LYS A 4 65.54 -173.70 REMARK 500 2 ASP A 6 -64.10 -141.19 REMARK 500 2 ASN A 7 146.86 -176.79 REMARK 500 2 GLU A 10 -155.44 -121.77 REMARK 500 2 ASP A 11 54.37 -96.81 REMARK 500 2 ALA A 12 60.67 64.64 REMARK 500 2 ALA A 14 -60.05 80.03 REMARK 500 2 TYR A 27 -72.61 -63.42 REMARK 500 2 ARG A 35 -75.77 -66.66 REMARK 500 3 SER A 3 125.82 -173.60 REMARK 500 3 ASP A 6 -62.77 -123.70 REMARK 500 3 ASN A 7 95.41 178.14 REMARK 500 3 ASP A 11 79.01 -173.42 REMARK 500 3 ALA A 14 -51.57 73.30 REMARK 500 3 TYR A 27 -74.07 -66.06 REMARK 500 3 ARG A 35 -76.68 -51.88 REMARK 500 4 LYS A 4 -58.24 171.78 REMARK 500 4 ASP A 11 -50.53 80.59 REMARK 500 4 ALA A 14 -49.78 77.49 REMARK 500 4 TYR A 27 -72.18 -58.80 REMARK 500 5 ASP A 6 174.87 68.02 REMARK 500 5 ASN A 7 85.43 59.99 REMARK 500 5 ASP A 11 89.97 -170.50 REMARK 500 5 ALA A 14 -58.07 77.01 REMARK 500 5 TYR A 27 -70.00 -62.81 REMARK 500 5 ARG A 35 -73.65 -90.82 REMARK 500 6 SER A 3 78.34 61.68 REMARK 500 6 GLU A 10 144.34 -174.79 REMARK 500 6 ASP A 11 87.20 61.92 REMARK 500 6 PRO A 13 -167.90 -75.73 REMARK 500 6 ALA A 14 -63.74 75.35 REMARK 500 6 TYR A 27 -73.78 -60.49 REMARK 500 7 LYS A 4 90.05 -37.40 REMARK 500 7 ASP A 6 102.99 -179.30 REMARK 500 7 ASN A 7 130.29 73.45 REMARK 500 7 GLU A 10 77.73 42.89 REMARK 500 7 ASP A 11 83.66 60.60 REMARK 500 7 ALA A 14 -61.40 74.26 REMARK 500 7 TYR A 27 -72.73 -60.97 REMARK 500 7 ARG A 35 -85.09 -115.33 REMARK 500 8 PRO A 2 -77.11 -82.13 REMARK 500 8 SER A 3 -48.46 -173.19 REMARK 500 8 LYS A 4 79.39 -170.78 REMARK 500 8 PRO A 5 82.36 -68.89 REMARK 500 8 ASP A 6 65.50 -175.16 REMARK 500 8 PRO A 8 -166.64 -69.44 REMARK 500 REMARK 500 THIS ENTRY HAS 114 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 2 TYR A 20 0.12 SIDE CHAIN REMARK 500 2 TYR A 21 0.13 SIDE CHAIN REMARK 500 4 TYR A 1 0.11 SIDE CHAIN REMARK 500 5 TYR A 1 0.11 SIDE CHAIN REMARK 500 5 TYR A 27 0.06 SIDE CHAIN REMARK 500 5 TYR A 36 0.09 SIDE CHAIN REMARK 500 8 TYR A 1 0.11 SIDE CHAIN REMARK 500 8 TYR A 20 0.10 SIDE CHAIN REMARK 500 9 TYR A 27 0.09 SIDE CHAIN REMARK 500 10 TYR A 20 0.10 SIDE CHAIN REMARK 500 10 TYR A 21 0.08 SIDE CHAIN REMARK 500 10 TYR A 27 0.15 SIDE CHAIN REMARK 500 11 TYR A 1 0.08 SIDE CHAIN REMARK 500 11 TYR A 20 0.07 SIDE CHAIN REMARK 500 12 TYR A 21 0.07 SIDE CHAIN REMARK 500 12 TYR A 27 0.09 SIDE CHAIN REMARK 500 13 TYR A 21 0.08 SIDE CHAIN REMARK 500 13 TYR A 27 0.14 SIDE CHAIN REMARK 500 13 TYR A 36 0.08 SIDE CHAIN REMARK 500 14 TYR A 21 0.08 SIDE CHAIN REMARK 500 14 TYR A 36 0.09 SIDE CHAIN REMARK 500 16 TYR A 20 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NH2 A 37 DBREF 1F8P A 1 36 UNP P01304 NEUY_PIG 1 36 SEQRES 1 A 37 TYR PRO SER LYS PRO ASP ASN PRO GLY GLU ASP ALA PRO SEQRES 2 A 37 ALA GLU ASP LEU ALA ARG TYR TYR SER ALA LEU ARG HIS SEQRES 3 A 37 TYR ILE ASN LEU ILE THR ARG GLN ARG TYR NH2 HET NH2 A 37 3 HETNAM NH2 AMINO GROUP FORMUL 1 NH2 H2 N HELIX 1 1 ASP A 16 TYR A 36 1 21 LINK C TYR A 36 N NH2 A 37 1555 1555 1.32 SITE 1 AC1 1 TYR A 36 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000