PDB Short entry for 1QFA HEADER HORMONE/GROWTH FACTOR 08-APR-99 1QFA TITLE STRUCTURE OF A NEUROPEPTIDE Y Y2 AGONIST COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (NEUROPEPTIDE Y); COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: NPY Y2 RECEPTOR AGONIST; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 OTHER_DETAILS: PEPTIDE N-TERMINALLY ACETYLATED AND C-TERMINALLY COMPND 8 AMIDATED. SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE SOURCE 4 OF THIS PEPTIDE IS NATURALLY FOUND IN HOMO SAPIENS (HUMAN). KEYWDS NEUROPEPTIDE Y, AGONIST, HELIX, HORMONE-GROWTH FACTOR COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR K.J.BARNHAM,F.CATALFAMO,P.K.PALLAGHY,G.J.HOWLETT,R.S.NORTON REVDAT 4 27-DEC-23 1QFA 1 REMARK SEQADV LINK REVDAT 3 14-MAR-18 1QFA 1 REMARK SEQADV REVDAT 2 24-FEB-09 1QFA 1 VERSN REVDAT 1 08-APR-00 1QFA 0 JRNL AUTH K.J.BARNHAM,F.CATALFAMO,P.K.PALLAGHY,G.J.HOWLETT,R.S.NORTON JRNL TITL HELICAL STRUCTURE AND SELF-ASSOCIATION IN A 13 RESIDUE JRNL TITL 2 NEUROPEPTIDE Y Y2 RECEPTOR AGONIST: RELATIONSHIP TO JRNL TITL 3 BIOLOGICAL ACTIVITY. JRNL REF BIOCHIM.BIOPHYS.ACTA V.1435 127 1999 JRNL REFN ISSN 0006-3002 JRNL PMID 10561544 JRNL DOI 10.1016/S0167-4838(99)00214-9 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1QFA COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-APR-99. REMARK 100 THE DEPOSITION ID IS D_1000000813. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 3.6 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 40% TFE-D3,60% WATER REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX600 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : DYANA, X-PLOR REMARK 210 METHOD USED : DISTANCE GEOMETRY REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1000 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST STEREOCHEMICAL AND NOE REMARK 210 ENERGIES REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL 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: 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 1 HIS A 26 NE2 HIS A 26 CD2 -0.067 REMARK 500 2 HIS A 26 NE2 HIS A 26 CD2 -0.069 REMARK 500 3 HIS A 26 NE2 HIS A 26 CD2 -0.067 REMARK 500 4 HIS A 26 NE2 HIS A 26 CD2 -0.067 REMARK 500 5 HIS A 26 NE2 HIS A 26 CD2 -0.068 REMARK 500 6 HIS A 26 NE2 HIS A 26 CD2 -0.068 REMARK 500 7 HIS A 26 NE2 HIS A 26 CD2 -0.067 REMARK 500 8 HIS A 26 NE2 HIS A 26 CD2 -0.068 REMARK 500 9 HIS A 26 NE2 HIS A 26 CD2 -0.067 REMARK 500 10 HIS A 26 NE2 HIS A 26 CD2 -0.067 REMARK 500 11 HIS A 26 NE2 HIS A 26 CD2 -0.068 REMARK 500 13 HIS A 26 NE2 HIS A 26 CD2 -0.067 REMARK 500 14 HIS A 26 NE2 HIS A 26 CD2 -0.066 REMARK 500 15 HIS A 26 NE2 HIS A 26 CD2 -0.066 REMARK 500 16 HIS A 26 NE2 HIS A 26 CD2 -0.068 REMARK 500 17 HIS A 26 NE2 HIS A 26 CD2 -0.068 REMARK 500 19 HIS A 26 NE2 HIS A 26 CD2 -0.067 REMARK 500 20 HIS A 26 NE2 HIS A 26 CD2 -0.068 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 5 ARG A 33 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 15 ARG A 33 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 16 ARG A 35 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 17 HIS A 26 -19.87 -47.13 REMARK 500 19 HIS A 26 -18.65 -49.02 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 ACE A 23 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NH2 A 37 DBREF 1QFA A 24 36 UNP P01303 NEUY_HUMAN 52 64 SEQADV 1QFA LEU A 28 UNP P01303 ILE 56 ENGINEERED MUTATION SEQADV 1QFA LEU A 31 UNP P01303 ILE 59 ENGINEERED MUTATION SEQRES 1 A 15 ACE LEU ARG HIS TYR LEU ASN LEU LEU THR ARG GLN ARG SEQRES 2 A 15 TYR NH2 HET ACE A 23 6 HET NH2 A 37 3 HETNAM ACE ACETYL GROUP HETNAM NH2 AMINO GROUP FORMUL 1 ACE C2 H4 O FORMUL 1 NH2 H2 N HELIX 1 1 ARG A 25 GLN A 34 1 10 LINK C ACE A 23 N LEU A 24 1555 1555 1.31 LINK C TYR A 36 N NH2 A 37 1555 1555 1.30 SITE 1 AC1 2 ARG A 25 HIS A 26 SITE 1 AC2 2 ARG A 35 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