10 20 30 40 50 60 70 80 1J9V - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER VIRAL PROTEIN 29-MAY-01 1J9V
TITLE SOLUTION STRUCTURE OF A LACTAM ANALOGUE (DABD) OF HIV GP41 TITLE 2 600-612 LOOP.
COMPND MOL_ID: 1; COMPND 2 MOLECULE: DABD (ACE)IWG(DAB)SGKLIDTTA 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 SOURCE 4 IN HIV GP41 GLYCOPROTEIN.
KEYWDS LACTAM PEPTIDE, LACTAM BOND, HIV, GP41, CYCLIC PEPTIDE, KEYWDS 2 VIRAL PROTEIN
EXPDTA SOLUTION NMR
NUMMDL 49
AUTHOR A.PHAN CHAN DU,D.LIMAL,V.SEMETEY,H.DALI,M.JOLIVET, AUTHOR 2 C.DESGRANGES,M.T.CUNG,J.P.BRIAND,M.C.PETIT,S.MULLER
REVDAT 2 24-FEB-09 1J9V 1 VERSN REVDAT 1 01-JUL-03 1J9V 0
JRNL AUTH A.P.DU,D.LIMAL,V.SEMETEY,H.DALI,M.JOLIVET, JRNL AUTH 2 C.DESGRANGES,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 JRNL TITL 3 THE 600-612 REGION OF THE HIV ENVELOPE GP41 JRNL TITL 4 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 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DYANA 1.5, DISCOVER 3 REMARK 3 AUTHORS : GUENTERT P., MUMENTHALER C. AND WUETHRICH K. REMARK 3 (1997) J. MOL. BIOL. 273, 283-298 (DYANA), REMARK 3 MOLECULAR SIMULATION INC. SAN DIEGO (DISCOVER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 50 INITIAL RANDOM STRUCTURES WERE REMARK 3 GENERATED USING SIMULATED ANNEALING IN DYANA SOFTWARE, REMARK 3 FOLLOWED BY 500PS RESTRAINED MINIMIZATION, 35PS MD IN VACUO AT REMARK 3 300K, 200 PS MD UNDER NMR RESTRAINTS AND 750 STEPS CONJUGATED REMARK 3 GRADIENT EM USING DISCOVER OF MSI SOFTWARE
REMARK 4 REMARK 4 1J9V COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JUN-01. REMARK 100 THE RCSB ID CODE IS RCSB013541.
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 : AMBIENT REMARK 210 SAMPLE CONTENTS : 3,5 MM PEPTIDE IN 500UL DMSO- REMARK 210 D6 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : DQF-COSY, 2D NOESY, 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 DINAMICS, REMARK 210 MOLECULAR DYNAMICS, 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: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D REMARK 210 HOMONUCLEAR TECHNIQUES. DIFFERENT NOESY EXPERIMENTS WITH REMARK 210 MIXING TIMES FROM 80 MS TO 800 MS 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 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 1-49 REMARK 470 RES CSSEQI ATOMS REMARK 470 ASP A 11 OD2
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 ND DAB A 5 CG ASP 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 0.152 REMARK 500 2 ALA A 14 C ALA A 14 OXT 0.152 REMARK 500 3 ALA A 14 C ALA A 14 OXT 0.154 REMARK 500 4 ALA A 14 C ALA A 14 OXT 0.155 REMARK 500 5 ALA A 14 C ALA A 14 OXT 0.155 REMARK 500 6 ALA A 14 C ALA A 14 OXT 0.154 REMARK 500 7 ALA A 14 C ALA A 14 OXT 0.155 REMARK 500 8 ALA A 14 C ALA A 14 OXT 0.154 REMARK 500 9 ALA A 14 C ALA A 14 OXT 0.154 REMARK 500 10 ALA A 14 C ALA A 14 OXT 0.153 REMARK 500 11 ALA A 14 C ALA A 14 OXT 0.145 REMARK 500 12 ALA A 14 C ALA A 14 OXT 0.145 REMARK 500 13 ALA A 14 C ALA A 14 OXT 0.144 REMARK 500 14 ALA A 14 C ALA A 14 OXT 0.142 REMARK 500 15 ALA A 14 C ALA A 14 OXT 0.142 REMARK 500 16 ALA A 14 C ALA A 14 OXT 0.142 REMARK 500 17 ALA A 14 C ALA A 14 OXT 0.142 REMARK 500 18 ALA A 14 C ALA A 14 OXT 0.141 REMARK 500 19 ALA A 14 C ALA A 14 OXT 0.145 REMARK 500 20 ALA A 14 C ALA A 14 OXT 0.143 REMARK 500 21 ALA A 14 C ALA A 14 OXT 0.144 REMARK 500 22 ALA A 14 C ALA A 14 OXT 0.143 REMARK 500 23 ALA A 14 C ALA A 14 OXT 0.143 REMARK 500 24 ALA A 14 C ALA A 14 OXT 0.144 REMARK 500 25 ALA A 14 C ALA A 14 OXT 0.143 REMARK 500 26 ALA A 14 C ALA A 14 OXT 0.143 REMARK 500 27 ALA A 14 C ALA A 14 OXT 0.142 REMARK 500 28 ALA A 14 C ALA A 14 OXT 0.142 REMARK 500 29 ALA A 14 C ALA A 14 OXT 0.143 REMARK 500 30 ALA A 14 C ALA A 14 OXT 0.143 REMARK 500 31 ALA A 14 C ALA A 14 OXT 0.142 REMARK 500 32 ALA A 14 C ALA A 14 OXT 0.143 REMARK 500 33 ALA A 14 C ALA A 14 OXT 0.144 REMARK 500 34 ALA A 14 C ALA A 14 OXT 0.144 REMARK 500 35 ALA A 14 C ALA A 14 OXT 0.144 REMARK 500 36 ALA A 14 C ALA A 14 OXT 0.145 REMARK 500 37 ALA A 14 C ALA A 14 OXT 0.146 REMARK 500 38 ALA A 14 C ALA A 14 OXT 0.146 REMARK 500 39 ALA A 14 C ALA A 14 OXT 0.147 REMARK 500 40 ALA A 14 C ALA A 14 OXT 0.147 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 0.145 REMARK 500 44 ALA A 14 C ALA A 14 OXT 0.142 REMARK 500 45 ALA A 14 C ALA A 14 OXT 0.143 REMARK 500 46 ALA A 14 C ALA A 14 OXT 0.143 REMARK 500 47 ALA A 14 C ALA A 14 OXT 0.143 REMARK 500 48 ALA A 14 C ALA A 14 OXT 0.143 REMARK 500 49 ALA A 14 C ALA A 14 OXT 0.143 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 LYS A 8 -67.51 -157.16 REMARK 500 2 LYS A 8 -67.63 -156.97 REMARK 500 3 LYS A 8 -67.46 -157.02 REMARK 500 4 LYS A 8 -66.57 -159.50 REMARK 500 5 LYS A 8 -66.55 -159.12 REMARK 500 6 LYS A 8 -67.53 -158.59 REMARK 500 7 LYS A 8 -67.31 -158.82 REMARK 500 8 LYS A 8 -61.20 -163.59 REMARK 500 9 LYS A 8 -66.85 -159.39 REMARK 500 10 LYS A 8 -66.66 -157.50 REMARK 500 11 LYS A 8 -67.73 -158.03 REMARK 500 11 THR A 12 -69.17 -94.06 REMARK 500 12 LYS A 8 -80.98 -142.69 REMARK 500 12 ASP A 11 76.44 -109.95 REMARK 500 13 LYS A 8 -70.38 -156.63 REMARK 500 14 LYS A 8 -68.09 -159.28 REMARK 500 14 THR A 12 -83.32 -98.78 REMARK 500 15 LYS A 8 -72.28 -150.88 REMARK 500 15 ASP A 11 75.50 -108.48 REMARK 500 15 THR A 12 -79.95 -80.52 REMARK 500 16 LYS A 8 -80.08 -139.82 REMARK 500 16 ASP A 11 73.42 -103.81 REMARK 500 17 LYS A 8 -68.65 -158.39 REMARK 500 17 THR A 12 -81.80 -97.41 REMARK 500 18 LYS A 8 -79.26 -146.55 REMARK 500 19 LYS A 8 -68.84 -159.06 REMARK 500 19 THR A 12 -83.29 -98.39 REMARK 500 20 LYS A 8 -68.66 -159.05 REMARK 500 21 LYS A 8 -72.11 -150.27 REMARK 500 21 THR A 12 -57.86 -132.86 REMARK 500 22 LYS A 8 -68.49 -132.15 REMARK 500 23 LYS A 8 -71.60 -146.68 REMARK 500 24 LYS A 8 -73.56 -142.80 REMARK 500 24 THR A 12 -52.12 -152.49 REMARK 500 24 THR A 13 -59.09 -128.21 REMARK 500 25 LYS A 8 -68.88 -135.72 REMARK 500 25 THR A 12 -50.40 -156.91 REMARK 500 26 LYS A 8 -64.87 -159.35 REMARK 500 26 THR A 12 -46.01 -158.28 REMARK 500 26 THR A 13 -64.74 -131.88 REMARK 500 27 LYS A 8 -57.88 -161.89 REMARK 500 27 THR A 12 -70.71 -151.09 REMARK 500 27 THR A 13 -66.12 -102.70 REMARK 500 28 LYS A 8 -57.60 -162.36 REMARK 500 28 THR A 12 -68.92 -152.07 REMARK 500 28 THR A 13 -66.56 -103.54 REMARK 500 29 LYS A 8 -66.28 -158.31 REMARK 500 29 THR A 12 -50.81 -158.06 REMARK 500 30 LYS A 8 -65.66 -158.56 REMARK 500 30 THR A 12 -46.05 -158.12 REMARK 500 30 THR A 13 -66.77 -130.42 REMARK 500 31 LYS A 8 -66.24 -158.15 REMARK 500 31 THR A 12 -47.07 -158.16 REMARK 500 31 THR A 13 -64.90 -131.12 REMARK 500 32 LYS A 8 -66.78 -157.71 REMARK 500 32 THR A 12 -47.34 -158.95 REMARK 500 32 THR A 13 -67.82 -126.55 REMARK 500 33 LYS A 8 -64.64 -156.92 REMARK 500 33 ASP A 11 65.51 -116.14 REMARK 500 33 THR A 12 -75.85 -156.01 REMARK 500 34 LYS A 8 -62.74 -158.82 REMARK 500 34 THR A 12 -65.85 -140.43 REMARK 500 35 LYS A 8 -74.94 -153.23 REMARK 500 36 LYS A 8 -74.18 -152.47 REMARK 500 37 LYS A 8 -75.28 -152.80 REMARK 500 38 LYS A 8 -75.32 -152.28 REMARK 500 39 LYS A 8 -74.90 -152.36 REMARK 500 40 LYS A 8 -80.22 -139.33 REMARK 500 41 LYS A 8 -80.98 -137.33 REMARK 500 42 LYS A 8 -67.73 -159.02 REMARK 500 43 LYS A 8 -69.25 -154.63 REMARK 500 43 THR A 12 -72.60 -73.62 REMARK 500 44 LYS A 8 -70.91 -153.49 REMARK 500 44 ASP A 11 68.93 -116.41 REMARK 500 44 THR A 12 -54.36 -152.76 REMARK 500 45 LYS A 8 -70.41 -154.92 REMARK 500 45 ASP A 11 69.99 -119.18 REMARK 500 45 THR A 12 -68.48 -155.19 REMARK 500 46 LYS A 8 -70.29 -154.95 REMARK 500 46 ASP A 11 70.16 -119.68 REMARK 500 46 THR A 12 -66.13 -154.24 REMARK 500 47 TRP A 3 22.76 -149.77 REMARK 500 47 LYS A 8 -77.79 -137.07 REMARK 500 47 LEU A 9 60.64 -115.29 REMARK 500 47 ASP A 11 75.00 -114.17 REMARK 500 47 THR A 12 -82.78 -145.51 REMARK 500 48 LYS A 8 -65.43 -158.42 REMARK 500 48 ASP A 11 71.53 -105.79 REMARK 500 49 LYS A 8 -67.84 -159.82 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 PEPTIDES COORDINATES. REMARK 900 RELATED ID: 1J8N RELATED DB: PDB REMARK 900 THE 1J8N ENTRY CONTAINS THE BETA3-SER ANALOGUE PEPTIDE REMARK 900 (HSER) REMARK 900 RELATED ID: 1J8Z RELATED DB: PDB REMARK 900 THE 1J8Z ENTRY CONTAINS THE BETA3-CYS ANALOGUE PEPTIDE REMARK 900 (HCYS)
DBREF 1J9V A 2 14 UNP P12488 ENV_HV1BN 591 603
SEQADV 1J9V ACE A 1 UNP P12488 INSERTION SEQADV 1J9V DAB A 5 UNP P12488 CYS 594 ENGINEERED SEQADV 1J9V ASP A 11 UNP P12488 CYS 600 ENGINEERED
SEQRES 1 A 14 ACE ILE TRP GLY DAB SER GLY LYS LEU ILE ASP THR THR SEQRES 2 A 14 ALA
MODRES 1J9V DAB A 5 ALA 2,4-DIAMINOBUTYRIC ACID
HET ACE A 1 6 HET DAB A 5 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 C GLY A 4 N DAB A 5 1555 1555 1.35 LINK C DAB A 5 N SER A 6 1555 1555 1.34
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