10 20 30 40 50 60 70 80 1JD8 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER VIRAL PROTEIN 13-JUN-01 1JD8
TITLE SOLUTION STRUCTURE OD LACTAM ANALOGUE DAPD OF HIV GP41 600- TITLE 2 612 LOOP.
COMPND MOL_ID: 1; COMPND 2 MOLECULE: ACETYL GROUP; 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 NATURALLY IN HIV GP41
KEYWDS CYCLIC PEPTIDE, GP41, HIV, LACTAM BOND, PSEUDOPEPTIDE, KEYWDS 2 VIRAL PROTEIN
EXPDTA SOLUTION NMR
NUMMDL 20
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 3 24-FEB-09 1JD8 1 VERSN REVDAT 2 25-MAY-04 1JD8 1 CHNID HET REVDAT 1 01-JUL-03 1JD8 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), MSI, REMARK 3 SAN DIEGO. (DISCOVER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 50 INITIAL STRUCTURES WERE GENERATED REMARK 3 USING DYANA SOFTWARE, FOLLOWED BY 500 STEPS RESTRAINED REMARK 3 MINIMIZATION.THEN USING DISCOVER 3, 35 PS MD AND 750 STEPS REMARK 3 CONJUGATE GRADIENT EM.
REMARK 4 REMARK 4 1JD8 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 RCSB ID CODE IS RCSB013646.
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 : ATMOSPHERIC ATM REMARK 210 SAMPLE CONTENTS : 4MM PEPTIDE IN 500 UL SOLVENT. 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 DYNAMICS, MOLECULAR REMARK 210 DYNAMICS, ENERGY MINIMIZATION. REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: CLASSICAL 2D HOMONUCLEAR NMR TECHNQUES WERE REMARK 210 USED.DIFFERENT NOESY WITH DIFFERENT MIXING TIME (FROM 80MS TO REMARK 210 800MS) WERE RECORDED IN ORDER TO DETERMINE THE BEST CONDITIONS REMARK 210 WITHOUT 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 1-20 REMARK 470 RES CSSEQI ATOMS REMARK 470 SET A 5 O 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 NT SET 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 0.141 REMARK 500 2 ALA A 14 C ALA A 14 OXT 0.142 REMARK 500 3 ALA A 14 C ALA A 14 OXT 0.138 REMARK 500 4 ALA A 14 C ALA A 14 OXT 0.141 REMARK 500 5 ALA A 14 C ALA A 14 OXT 0.141 REMARK 500 6 ALA A 14 C ALA A 14 OXT 0.139 REMARK 500 7 ALA A 14 C ALA A 14 OXT 0.145 REMARK 500 8 ALA A 14 C ALA A 14 OXT 0.141 REMARK 500 9 ALA A 14 C ALA A 14 OXT 0.140 REMARK 500 10 ALA A 14 C ALA A 14 OXT 0.145 REMARK 500 11 ALA A 14 C ALA A 14 OXT 0.145 REMARK 500 12 ALA A 14 C ALA A 14 OXT 0.141 REMARK 500 13 ALA A 14 C ALA A 14 OXT 0.143 REMARK 500 14 ALA A 14 C ALA A 14 OXT 0.141 REMARK 500 15 ALA A 14 C ALA A 14 OXT 0.141 REMARK 500 16 ALA A 14 C ALA A 14 OXT 0.141 REMARK 500 17 ALA A 14 C ALA A 14 OXT 0.145 REMARK 500 18 ALA A 14 C ALA A 14 OXT 0.141 REMARK 500 19 ALA A 14 C ALA A 14 OXT 0.140 REMARK 500 20 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 -84.61 -158.03 REMARK 500 1 THR A 13 79.82 -100.20 REMARK 500 2 LYS A 8 -85.88 -152.98 REMARK 500 3 LYS A 8 -82.29 -160.73 REMARK 500 3 THR A 12 108.48 -56.00 REMARK 500 4 LYS A 8 -94.93 -153.47 REMARK 500 4 THR A 12 102.93 -57.84 REMARK 500 5 LYS A 8 -92.03 -154.53 REMARK 500 5 THR A 12 99.48 -69.39 REMARK 500 6 LYS A 8 -85.48 -158.46 REMARK 500 6 THR A 12 108.04 -56.88 REMARK 500 7 LYS A 8 -90.32 -159.91 REMARK 500 8 LYS A 8 -95.03 -159.90 REMARK 500 9 LYS A 8 -90.62 -155.06 REMARK 500 10 LYS A 8 -92.36 -150.87 REMARK 500 10 THR A 12 105.72 -59.46 REMARK 500 11 LYS A 8 -90.85 -148.06 REMARK 500 12 LYS A 8 -85.81 -157.75 REMARK 500 12 THR A 13 -65.04 -93.43 REMARK 500 13 LYS A 8 -89.19 -155.57 REMARK 500 13 THR A 13 -69.42 -97.53 REMARK 500 14 LYS A 8 -89.53 -156.20 REMARK 500 14 THR A 13 -73.36 -130.65 REMARK 500 15 LYS A 8 -99.34 -156.30 REMARK 500 16 LYS A 8 -93.57 -152.49 REMARK 500 16 THR A 12 104.37 -58.51 REMARK 500 16 THR A 13 -72.72 -140.87 REMARK 500 17 LYS A 8 -91.36 -159.50 REMARK 500 18 LYS A 8 -91.65 -161.90 REMARK 500 19 LYS A 8 -94.38 -158.81 REMARK 500 19 THR A 13 -73.09 -142.33 REMARK 500 20 LYS A 8 -92.43 -154.29 REMARK 500 20 THR A 13 -77.08 -132.04 REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1IM7 RELATED DB: PDB REMARK 900 1IM7 CONTAINS THE PARENT PEPTIDE REMARK 900 RELATED ID: 1J8N RELATED DB: PDB REMARK 900 1J8N CONTAINS THE BETA3-SER ANALOGUE PEPTIDE (HSER) REMARK 900 RELATED ID: 1J8Z RELATED DB: PDB REMARK 900 1J8Z CONTAINS THE BETA3-CYS ANALOGUE PEPTIDE (HCYS) REMARK 900 RELATED ID: 1J9V RELATED DB: PDB REMARK 900 1J9V CONTAINS THE LACTAM ANALOGUE PEPTIDE DABD REMARK 900 RELATED ID: 1JAR RELATED DB: PDB REMARK 900 1JAR CONTAINS THE LACTAM ANALOGUE PEPTIDEV DDAB REMARK 900 RELATED ID: 1JC8 RELATED DB: PDB REMARK 900 1JC8 CONTAINS THE LACTAM ANALOGUE PEPTIDE DDAP REMARK 900 RELATED ID: 1JAA RELATED DB: PDB REMARK 900 1JAA CONTAINS THE LACTAM ANALOGUE PEPTIDE DAPE REMARK 900 RELATED ID: 1JCP RELATED DB: PDB REMARK 900 1JCP CONTAINS THE LACTAM ANALOGUE PEPTIDE EDAP
DBREF 1JD8 A 1 14 PDB 1JD8 1JD8 1 14
SEQRES 1 A 14 ACE ILE TRP GLY SET SER GLY LYS LEU ILE ASP THR THR SEQRES 2 A 14 ALA
MODRES 1JD8 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
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