HEADER VIRAL PROTEIN 30-MAY-01 1JAA TITLE SOLUTION STRUCTURE OF LACTAM ANALOGUE (DAPE) OF HIV GP41 600-612 LOOP. COMPND MOL_ID: 1; COMPND 2 MOLECULE: DAPE : (ACE)IWG(DAP)SGKLIETTA ANALOGUE OF HIV GP41; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE PARENT PEPTIDE (IWGCSGKLICTTA) OCCURS NATURALLY SOURCE 4 IN HIV GP41 GLYCOPROTEIN KEYWDS LACTAM BOND, CYCLIC PEPTIDE, PEPTIDOMIMETICS, GP41, HIV, VIRAL KEYWDS 2 PROTEIN EXPDTA SOLUTION NMR NUMMDL 50 AUTHOR A.PHAN CHAN DU,D.LIMAL,V.SEMETEY,H.DALI,M.JOLIVET,C.DESGRANGES, AUTHOR 2 M.T.CUNG,J.P.BRIAND,M.C.PETIT,S.MULLER REVDAT 3 27-OCT-21 1JAA 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 1JAA 1 VERSN REVDAT 1 01-JUL-03 1JAA 0 JRNL AUTH A.P.DU,D.LIMAL,V.SEMETEY,H.DALI,M.JOLIVET,C.DESGRANGES, JRNL AUTH 2 M.T.CUNG,J.P.BRIAND,M.C.PETIT,S.MULLER JRNL TITL STRUCTURAL AND IMMUNOLOGICAL CHARACTERISATION OF JRNL TITL 2 HETEROCLITIC PEPTIDE ANALOGUES CORRESPONDING TO THE 600-612 JRNL TITL 3 REGION OF THE HIV ENVELOPE GP41 GLYCOPROTEIN. JRNL REF J.MOL.BIOL. V. 323 503 2002 JRNL REFN ISSN 0022-2836 JRNL PMID 12381305 JRNL DOI 10.1016/S0022-2836(02)00701-5 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.6, DYANA 1.5, DISCOVER 3 REMARK 3 AUTHORS : BRUKER GMBH (XWINNMR), GUENTERT P., MUMETHALER REMARK 3 C.AND WUETHRICH K. (1997) J. MOL. BIOL., 273, 283- REMARK 3 298 (DYANA), MOLECULAR SIMULATION INC., SAN DIEGO REMARK 3 (DISCOVER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 50 INITIAL RANDOM STRUCTURE WERE REMARK 3 GENERATD IN DYANA SOFTWARE , FOLLOWED BY 500 PS RESTRAINED REMARK 3 MINIMIZATION + 35 PS MD IN VACUO AT 300K, 200 PS UNDER NMR REMARK 3 RESTRAINTS AND 750PS CONJUGATED GRADIENT EM USING THE DISCOVER REMARK 3 MODULE OF MSI SOFTWARE REMARK 4 REMARK 4 1JAA COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-JUN-01. REMARK 100 THE DEPOSITION ID IS D_1000013556. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : NULL REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIANT REMARK 210 SAMPLE CONTENTS : 3 MM PEPTIDE IN 500 UL DMSO-D6 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY; TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 400 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 2.6, XEASY 1.2 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 MOLECULAR DYNAMICS, ENERGY REMARK 210 MINIMIZATION. REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 50 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR REMARK 210 TECHNIQUES. DIFFERENT NOESY EXPERIMENTS , WITH MIXING TIMES FROM REMARK 210 80 MS TO 800 MS , WERE RECORDED IN ORDER TO DETERMINED THE BEST REMARK 210 CONDITIONS AVOIDING SPIN DIFFUSION. 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 MODELS 1-50 REMARK 470 RES CSSEQI ATOMS REMARK 470 SET A 5 O REMARK 470 GLU A 11 OE2 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 NT SET A 5 CD GLU A 11 1.34 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 1 ALA A 14 C ALA A 14 OXT 0.141 REMARK 500 2 ALA A 14 C ALA A 14 OXT 0.145 REMARK 500 3 ALA A 14 C ALA A 14 OXT 0.144 REMARK 500 4 ALA A 14 C ALA A 14 OXT 0.143 REMARK 500 5 ALA A 14 C ALA A 14 OXT 0.144 REMARK 500 6 ALA A 14 C ALA A 14 OXT 0.142 REMARK 500 7 ALA A 14 C ALA A 14 OXT 0.144 REMARK 500 8 ALA A 14 C ALA A 14 OXT 0.144 REMARK 500 9 ALA A 14 C ALA A 14 OXT 0.143 REMARK 500 10 ALA A 14 C ALA A 14 OXT 0.145 REMARK 500 11 ALA A 14 C ALA A 14 OXT 0.144 REMARK 500 12 ALA A 14 C ALA A 14 OXT 0.141 REMARK 500 13 ALA A 14 C ALA A 14 OXT 0.140 REMARK 500 14 ALA A 14 C ALA A 14 OXT 0.142 REMARK 500 15 ALA A 14 C ALA A 14 OXT 0.141 REMARK 500 16 ALA A 14 C ALA A 14 OXT 0.145 REMARK 500 17 ALA A 14 C ALA A 14 OXT 0.144 REMARK 500 18 ALA A 14 C ALA A 14 OXT 0.144 REMARK 500 19 ALA A 14 C ALA A 14 OXT 0.144 REMARK 500 20 ALA A 14 C ALA A 14 OXT 0.144 REMARK 500 21 ALA A 14 C ALA A 14 OXT 0.140 REMARK 500 22 ALA A 14 C ALA A 14 OXT 0.146 REMARK 500 23 ALA A 14 C ALA A 14 OXT 0.143 REMARK 500 24 ALA A 14 C ALA A 14 OXT 0.143 REMARK 500 25 ALA A 14 C ALA A 14 OXT 0.141 REMARK 500 26 ALA A 14 C ALA A 14 OXT 0.145 REMARK 500 27 ALA A 14 C ALA A 14 OXT 0.145 REMARK 500 28 ALA A 14 C ALA A 14 OXT 0.146 REMARK 500 29 ALA A 14 C ALA A 14 OXT 0.141 REMARK 500 30 ALA A 14 C ALA A 14 OXT 0.140 REMARK 500 31 ALA A 14 C ALA A 14 OXT 0.142 REMARK 500 32 ALA A 14 C ALA A 14 OXT 0.142 REMARK 500 33 ALA A 14 C ALA A 14 OXT 0.145 REMARK 500 34 ALA A 14 C ALA A 14 OXT 0.141 REMARK 500 35 ALA A 14 C ALA A 14 OXT 0.141 REMARK 500 36 ALA A 14 C ALA A 14 OXT 0.144 REMARK 500 37 ALA A 14 C ALA A 14 OXT 0.145 REMARK 500 38 ALA A 14 C ALA A 14 OXT 0.141 REMARK 500 39 ALA A 14 C ALA A 14 OXT 0.144 REMARK 500 40 ALA A 14 C ALA A 14 OXT 0.141 REMARK 500 41 ALA A 14 C ALA A 14 OXT 0.145 REMARK 500 42 ALA A 14 C ALA A 14 OXT 0.146 REMARK 500 43 ALA A 14 C ALA A 14 OXT 0.145 REMARK 500 44 ALA A 14 C ALA A 14 OXT 0.145 REMARK 500 45 ALA A 14 C ALA A 14 OXT 0.145 REMARK 500 46 ALA A 14 C ALA A 14 OXT 0.145 REMARK 500 47 ALA A 14 C ALA A 14 OXT 0.146 REMARK 500 48 ALA A 14 C ALA A 14 OXT 0.145 REMARK 500 49 ALA A 14 C ALA A 14 OXT 0.146 REMARK 500 50 ALA A 14 C ALA A 14 OXT 0.143 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 8 TRP A 3 CD1 - NE1 - CE2 ANGL. DEV. = -5.5 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 ILE A 10 81.58 -161.50 REMARK 500 1 THR A 13 -66.52 -125.62 REMARK 500 2 TRP A 3 64.87 -151.72 REMARK 500 2 ILE A 10 73.99 -156.87 REMARK 500 2 GLU A 11 55.78 -153.82 REMARK 500 2 THR A 13 -77.25 -136.82 REMARK 500 3 ILE A 10 81.33 -150.38 REMARK 500 3 GLU A 11 72.71 -150.71 REMARK 500 4 ILE A 10 83.72 -156.91 REMARK 500 4 THR A 13 -76.95 -143.20 REMARK 500 5 ILE A 10 80.74 -151.94 REMARK 500 5 GLU A 11 52.66 -148.51 REMARK 500 5 THR A 13 -84.46 -133.19 REMARK 500 6 ILE A 10 76.79 -151.32 REMARK 500 6 THR A 13 -74.53 -148.37 REMARK 500 7 GLU A 11 61.76 -157.35 REMARK 500 7 THR A 13 -72.04 -135.11 REMARK 500 8 ILE A 10 79.85 -153.05 REMARK 500 8 THR A 13 -76.05 -136.56 REMARK 500 9 ILE A 10 81.31 -151.29 REMARK 500 10 GLU A 11 67.44 -155.26 REMARK 500 11 GLU A 11 36.05 -141.55 REMARK 500 11 THR A 12 74.99 -157.43 REMARK 500 11 THR A 13 -74.12 -139.06 REMARK 500 12 GLU A 11 41.13 -101.17 REMARK 500 12 THR A 12 -73.73 -148.11 REMARK 500 14 ILE A 10 60.31 -118.05 REMARK 500 14 GLU A 11 58.55 -119.00 REMARK 500 14 THR A 12 -77.85 -139.80 REMARK 500 15 GLU A 11 58.88 -102.25 REMARK 500 15 THR A 12 -72.09 -148.23 REMARK 500 16 GLU A 11 55.48 -113.49 REMARK 500 16 THR A 12 -76.05 -151.20 REMARK 500 17 GLU A 11 67.35 -117.44 REMARK 500 17 THR A 12 -73.46 -96.17 REMARK 500 18 ILE A 10 62.29 -117.34 REMARK 500 18 GLU A 11 53.96 -112.01 REMARK 500 18 THR A 12 -75.69 -148.48 REMARK 500 19 TRP A 3 71.10 -110.17 REMARK 500 20 TRP A 3 58.50 -119.24 REMARK 500 20 ILE A 10 70.80 -117.46 REMARK 500 20 GLU A 11 70.69 -114.60 REMARK 500 20 THR A 12 -66.70 -98.23 REMARK 500 21 GLU A 11 53.35 -113.20 REMARK 500 21 THR A 12 -75.98 -148.61 REMARK 500 22 TRP A 3 73.09 -116.38 REMARK 500 22 ILE A 10 76.05 -110.14 REMARK 500 22 GLU A 11 69.74 -101.41 REMARK 500 23 TRP A 3 78.21 -155.67 REMARK 500 23 THR A 12 -70.75 -77.50 REMARK 500 REMARK 500 THIS ENTRY HAS 95 RAMACHANDRAN OUTLIERS. 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 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1IM7 RELATED DB: PDB REMARK 900 THE 1IM7 PDB ENTRY CONTAINS THE PARENT PEPTIDE. REMARK 900 RELATED ID: 1J8N RELATED DB: PDB REMARK 900 THE 1J8N PDB ENTRY CONTAINS THE BETA3-SER ANALOGUE PEPTIDE (HSER) REMARK 900 RELATED ID: 1J8Z RELATED DB: PDB REMARK 900 THE 1J8Z PDB ENTRY CONTAINS THE BETA3-CYS ANLOGUE PEPTIDE (HCYS) REMARK 900 RELATED ID: 1J9V RELATED DB: PDB REMARK 900 THE 1J9V PDB ENTRY CONTAINS THE LACTAM ANALOGUE DABD. DBREF 1JAA A 2 14 UNP P12488 ENV_HV1BN 591 603 SEQADV 1JAA ACE A 1 UNP P12488 ACETYLATION SEQADV 1JAA SET A 5 UNP P12488 CYS 594 ENGINEERED MUTATION SEQADV 1JAA GLU A 11 UNP P12488 CYS 600 ENGINEERED MUTATION SEQRES 1 A 14 ACE ILE TRP GLY SET SER GLY LYS LEU ILE GLU THR THR SEQRES 2 A 14 ALA MODRES 1JAA SET A 5 SER AMINOSERINE HET ACE A 1 6 HET SET A 5 11 HETNAM ACE ACETYL GROUP HETNAM SET AMINOSERINE FORMUL 1 ACE C2 H4 O FORMUL 1 SET C3 H8 N2 O2 LINK C ACE A 1 N ILE A 2 1555 1555 1.34 LINK C GLY A 4 N SET A 5 1555 1555 1.35 LINK CB SET A 5 N SER A 6 1555 1555 1.35 SITE 1 AC1 1 GLU A 11 CRYST1 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 MODEL 1 HETATM 1 C ACE A 1 2.979 4.725 0.291 1.00 0.00 C HETATM 2 O ACE A 1 2.367 3.722 0.664 1.00 0.00 O HETATM 3 CH3 ACE A 1 2.229 5.889 -0.348 1.00 0.00 C HETATM 4 H1 ACE A 1 2.354 6.820 0.238 1.00 0.00 H HETATM 5 H2 ACE A 1 2.582 6.083 -1.378 1.00 0.00 H HETATM 6 H3 ACE A 1 1.145 5.681 -0.404 1.00 0.00 H