HEADER VIRAL PROTEIN 31-MAY-01 1JAR TITLE SOLUTION STRUCTURE OF LACTAM ANALOGUE (DDAB)OF HIV GP41 600-612 LOOP. COMPND MOL_ID: 1; COMPND 2 MOLECULE: DDAB: (ACE)IWGDSGKLI(DAB)TTA ANALOGUE OF HIV GP41; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1 KEYWDS LACTAM BOND, CYCLIC PEPTIDE, HIV GP41, PEPTIDOMIMETICS., VIRAL KEYWDS 2 PROTEIN EXPDTA SOLUTION NMR NUMMDL 49 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 1JAR 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 1JAR 1 VERSN REVDAT 1 01-JUL-03 1JAR 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., MUMENTHALER 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 RADOM STRUCTURE ARE REMARK 3 GENERATED USING DYANA SOFTWARE.FOLLOWED BY 500 PS RESTRAINED REMARK 3 MINIMIZATION. FOLLOWED BY 750 PS CONJUGATED GRADIENT EM USING REMARK 3 THE DISCOVER MODULE OF MSI SOFTWARE. REMARK 4 REMARK 4 1JAR 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_1000013563. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : NULL REMARK 210 IONIC STRENGTH : NONE REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 4MM PEPTIDE IN 500UL 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 DYNALMICS, REMARK 210 MOLECULAR DYNANMICS, ENERGY REMARK 210 MINIMIZATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 49 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS CALCULATED USING STANDARD 2D HOMONUCLEAR REMARK 210 TECHNIQUES. DIFFERENT NOSY EXPERIMENTS WERE RECORDED IN ORDER TO REMARK 210 DETERMINED THE BEST 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 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 0.143 REMARK 500 2 ALA A 14 C ALA A 14 OXT 0.143 REMARK 500 3 ALA A 14 C ALA A 14 OXT 0.143 REMARK 500 4 ALA A 14 C ALA A 14 OXT 0.146 REMARK 500 5 ALA A 14 C ALA A 14 OXT 0.145 REMARK 500 6 ALA A 14 C ALA A 14 OXT 0.145 REMARK 500 7 ALA A 14 C ALA A 14 OXT 0.146 REMARK 500 8 ALA A 14 C ALA A 14 OXT 0.145 REMARK 500 9 ALA A 14 C ALA A 14 OXT 0.147 REMARK 500 10 ALA A 14 C ALA A 14 OXT 0.144 REMARK 500 11 ALA A 14 C ALA A 14 OXT 0.143 REMARK 500 12 ALA A 14 C ALA A 14 OXT 0.144 REMARK 500 13 ALA A 14 C ALA A 14 OXT 0.142 REMARK 500 14 ALA A 14 C ALA A 14 OXT 0.144 REMARK 500 15 ALA A 14 C ALA A 14 OXT 0.144 REMARK 500 16 ALA A 14 C ALA A 14 OXT 0.143 REMARK 500 17 ALA A 14 C ALA A 14 OXT 0.144 REMARK 500 18 ALA A 14 C ALA A 14 OXT 0.143 REMARK 500 19 ALA A 14 C ALA A 14 OXT 0.143 REMARK 500 20 ALA A 14 C ALA A 14 OXT 0.146 REMARK 500 21 ALA A 14 C ALA A 14 OXT 0.145 REMARK 500 22 ALA A 14 C ALA A 14 OXT 0.144 REMARK 500 23 ALA A 14 C ALA A 14 OXT 0.144 REMARK 500 24 ALA A 14 C ALA A 14 OXT 0.141 REMARK 500 25 ALA A 14 C ALA A 14 OXT 0.141 REMARK 500 26 ALA A 14 C ALA A 14 OXT 0.141 REMARK 500 27 ALA A 14 C ALA A 14 OXT 0.141 REMARK 500 28 ALA A 14 C ALA A 14 OXT 0.141 REMARK 500 29 ALA A 14 C ALA A 14 OXT 0.142 REMARK 500 30 ALA A 14 C ALA A 14 OXT 0.142 REMARK 500 31 ALA A 14 C ALA A 14 OXT 0.142 REMARK 500 32 ALA A 14 C ALA A 14 OXT 0.141 REMARK 500 33 ALA A 14 C ALA A 14 OXT 0.141 REMARK 500 34 ALA A 14 C ALA A 14 OXT 0.142 REMARK 500 35 ALA A 14 C ALA A 14 OXT 0.141 REMARK 500 36 ALA A 14 C ALA A 14 OXT 0.146 REMARK 500 37 ALA A 14 C ALA A 14 OXT 0.145 REMARK 500 38 ALA A 14 C ALA A 14 OXT 0.143 REMARK 500 39 ALA A 14 C ALA A 14 OXT 0.143 REMARK 500 40 ALA A 14 C ALA A 14 OXT 0.144 REMARK 500 41 ALA A 14 C ALA A 14 OXT 0.143 REMARK 500 42 ALA A 14 C ALA A 14 OXT 0.144 REMARK 500 43 ALA A 14 C ALA A 14 OXT 0.144 REMARK 500 44 ALA A 14 C ALA A 14 OXT 0.146 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 0.147 REMARK 500 48 ALA A 14 C ALA A 14 OXT 0.143 REMARK 500 49 ALA A 14 C ALA A 14 OXT 0.144 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 THR A 12 -85.21 -72.69 REMARK 500 2 THR A 13 -73.70 -124.50 REMARK 500 7 THR A 13 -69.90 -91.55 REMARK 500 12 ILE A 10 82.02 -158.28 REMARK 500 15 TRP A 3 68.49 -112.32 REMARK 500 19 ILE A 10 83.68 -154.11 REMARK 500 20 SER A 6 85.72 -158.93 REMARK 500 20 ILE A 10 86.40 -152.46 REMARK 500 22 TRP A 3 50.80 -114.01 REMARK 500 22 ILE A 10 86.09 -156.40 REMARK 500 23 SER A 6 85.84 -156.24 REMARK 500 30 ILE A 10 70.52 -163.59 REMARK 500 31 ILE A 10 70.19 -163.23 REMARK 500 32 ILE A 10 69.93 -161.66 REMARK 500 33 ILE A 10 68.88 -160.61 REMARK 500 34 ILE A 10 70.57 -164.74 REMARK 500 35 ILE A 10 70.78 -162.41 REMARK 500 36 ILE A 10 67.77 -160.03 REMARK 500 37 ILE A 10 67.93 -161.85 REMARK 500 38 ILE A 10 72.26 -154.40 REMARK 500 39 ILE A 10 81.67 -160.40 REMARK 500 40 ILE A 10 80.08 -161.34 REMARK 500 41 ILE A 10 74.14 -158.12 REMARK 500 42 ILE A 10 68.41 -163.07 REMARK 500 43 ILE A 10 75.33 -151.54 REMARK 500 43 DAB A 11 61.24 -104.22 REMARK 500 45 ILE A 10 55.61 -145.05 REMARK 500 46 ILE A 10 73.12 -161.25 REMARK 500 47 ILE A 10 75.44 -159.09 REMARK 500 47 DAB A 11 52.81 -105.06 REMARK 500 48 ILE A 10 77.99 -151.42 REMARK 500 48 DAB A 11 69.67 -115.52 REMARK 500 49 ILE A 10 77.18 -162.07 REMARK 500 49 DAB A 11 71.59 -112.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1IM7 RELATED DB: PDB REMARK 900 THE 1IM7 ENTRY CONTAINS THE PARENT PEPTIDE. REMARK 900 RELATED ID: 1J8N RELATED DB: PDB REMARK 900 THE 1J8N ENTRY CONTAINS THE BETA3-SER CONTAING ANALOGUE (HSER) REMARK 900 RELATED ID: 1J8Z RELATED DB: PDB REMARK 900 THE 1J8Z ENTRY CONTAINS THE BETA3-CYS CONTAING ANALOGUE PEPTIDE REMARK 900 (HCYS) REMARK 900 RELATED ID: 1J9V RELATED DB: PDB REMARK 900 THE 1J9V ENTRY CONTAINS THE LACTAM ANALOGUE DABD REMARK 900 RELATED ID: 1JAA RELATED DB: PDB REMARK 900 THE 1JAA ENTRY CONTAINS THE LACTAM ANALOGUE DAPE DBREF 1JAR A 2 14 UNP P12488 ENV_HV1BN 591 603 SEQADV 1JAR ACE A 1 UNP P12488 ACETYLATION SEQADV 1JAR ASP A 5 UNP P12488 CYS 594 ENGINEERED MUTATION SEQADV 1JAR DAB A 11 UNP P12488 CYS 600 ENGINEERED MUTATION SEQRES 1 A 14 ACE ILE TRP GLY ASP SER GLY LYS LEU ILE DAB THR THR SEQRES 2 A 14 ALA MODRES 1JAR DAB A 11 ALA 2,4-DIAMINOBUTYRIC ACID HET ACE A 1 6 HET DAB A 11 14 HETNAM ACE ACETYL GROUP HETNAM DAB 2,4-DIAMINOBUTYRIC ACID FORMUL 1 ACE C2 H4 O FORMUL 1 DAB C4 H10 N2 O2 LINK C ACE A 1 N ILE A 2 1555 1555 1.34 LINK CG ASP A 5 ND DAB A 11 1555 1555 1.34 LINK C ILE A 10 N DAB A 11 1555 1555 1.35 LINK C DAB A 11 N THR A 12 1555 1555 1.36 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 -1.622 6.333 7.883 1.00 0.00 C HETATM 2 O ACE A 1 -0.451 6.134 8.217 1.00 0.00 O HETATM 3 CH3 ACE A 1 -2.643 6.836 8.899 1.00 0.00 C HETATM 4 H1 ACE A 1 -2.184 6.960 9.896 1.00 0.00 H HETATM 5 H2 ACE A 1 -3.057 7.818 8.603 1.00 0.00 H HETATM 6 H3 ACE A 1 -3.485 6.128 9.011 1.00 0.00 H