HEADER VIRAL PROTEIN 08-JUN-01 1JC8 TITLE SOLUTION STRUCTURE OF LACTAM ANALOGUE (DDAP) OF GP41 600-612 LOOP OF TITLE 2 HIV COMPND MOL_ID: 1; COMPND 2 MOLECULE: DDAP: (ACE)IWGDSGKLI(DNP)TTA ANALOGUE OF HIV GP41; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: ATOM OD2 OF ASP 5 IS MISSING DUE TO THE SIDE-CHAIN COMPND 6 LINK BETWEEN ASP 5 AND DNP 11 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, HIV GP41, PEPTIDOMIMETICS., VIRAL KEYWDS 2 PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 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 1JC8 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 1JC8 1 VERSN REVDAT 1 01-JUL-03 1JC8 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), MSI, SAN DIEGO (DISCOVER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 50 INITIAL RANDOM STRUCTURES WERE REMARK 3 GENERATED USIN DYANA SOFTWARE, FOLLOWED BY 500PS RESTRAINED REMARK 3 MINIMIZATION, 35PS MD AND 750PS CONJUGATED GRADIENT EM USING REMARK 3 DISCOVER MODULE OF MSI SOFTWARE. REMARK 4 REMARK 4 1JC8 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_1000013613. 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 : 2MM PEPTIDE IN 500UL 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 ANGLES DYNAMICS, REMARK 210 MOLECULAR DYNAMICS, ENERGY REMARK 210 MINIMIZATION. REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: CLASSICAL 2D HOMONUCLEAR NMR TECHNIQUES WERE USED. REMARK 210 DIFFERENT NOESY EXPERIMENTS WITH DIFFERENT MIXING TIMES FROM REMARK 210 80MS TO 800MS WERE RECORDED IN ORDER TO DETERMINE BEST REMARK 210 CONDITIONS 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 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 1-20 REMARK 470 RES CSSEQI ATOMS REMARK 470 ASP A 5 OD2 REMARK 470 SET A 11 O 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 CG ASP A 5 NT SET 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 0.142 REMARK 500 2 ALA A 14 C ALA A 14 OXT 0.144 REMARK 500 3 ALA A 14 C ALA A 14 OXT 0.143 REMARK 500 4 ALA A 14 C ALA A 14 OXT 0.143 REMARK 500 5 ALA A 14 C ALA A 14 OXT 0.146 REMARK 500 6 ALA A 14 C ALA A 14 OXT 0.141 REMARK 500 7 ALA A 14 C ALA A 14 OXT 0.141 REMARK 500 8 ALA A 14 C ALA A 14 OXT 0.141 REMARK 500 9 ALA A 14 C ALA A 14 OXT 0.141 REMARK 500 10 ALA A 14 C ALA A 14 OXT 0.141 REMARK 500 11 ALA A 14 C ALA A 14 OXT 0.141 REMARK 500 12 ALA A 14 C ALA A 14 OXT 0.142 REMARK 500 13 ALA A 14 C ALA A 14 OXT 0.141 REMARK 500 14 ALA A 14 C ALA A 14 OXT 0.141 REMARK 500 15 ALA A 14 C ALA A 14 OXT 0.142 REMARK 500 16 ALA A 14 C ALA A 14 OXT 0.141 REMARK 500 17 ALA A 14 C ALA A 14 OXT 0.141 REMARK 500 18 ALA A 14 C ALA A 14 OXT 0.142 REMARK 500 19 ALA A 14 C ALA A 14 OXT 0.141 REMARK 500 20 ALA A 14 C ALA A 14 OXT 0.141 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 -71.97 -157.92 REMARK 500 1 LEU A 9 -77.57 -135.17 REMARK 500 2 LYS A 8 -69.44 -159.00 REMARK 500 2 LEU A 9 -74.38 -141.88 REMARK 500 3 LEU A 9 -71.43 -145.14 REMARK 500 4 LYS A 8 -69.80 -160.40 REMARK 500 4 LEU A 9 -73.34 -142.26 REMARK 500 5 LYS A 8 -73.11 -161.12 REMARK 500 5 LEU A 9 -73.04 -138.85 REMARK 500 6 LYS A 8 -75.78 -159.62 REMARK 500 6 LEU A 9 -73.05 -133.56 REMARK 500 7 LYS A 8 -75.01 -159.92 REMARK 500 7 LEU A 9 -71.93 -133.92 REMARK 500 8 LEU A 9 -69.08 -137.37 REMARK 500 9 LYS A 8 -76.17 -160.16 REMARK 500 9 LEU A 9 -72.79 -134.75 REMARK 500 10 LYS A 8 -70.87 -161.33 REMARK 500 10 LEU A 9 -72.86 -140.83 REMARK 500 11 TRP A 3 -64.48 -90.39 REMARK 500 11 LYS A 8 -70.89 -161.44 REMARK 500 11 LEU A 9 -74.32 -138.62 REMARK 500 12 LYS A 8 -75.12 -158.79 REMARK 500 12 LEU A 9 -72.92 -134.75 REMARK 500 13 LEU A 9 -77.06 -143.86 REMARK 500 14 LYS A 8 -65.69 -145.52 REMARK 500 14 LEU A 9 -69.62 -152.60 REMARK 500 14 THR A 13 79.98 -106.34 REMARK 500 15 LYS A 8 -70.00 -159.60 REMARK 500 15 LEU A 9 -73.76 -139.79 REMARK 500 16 LYS A 8 -68.76 -159.90 REMARK 500 16 LEU A 9 -73.95 -141.99 REMARK 500 17 LYS A 8 -63.29 -158.90 REMARK 500 17 LEU A 9 -74.02 -142.32 REMARK 500 18 LYS A 8 -67.12 -159.69 REMARK 500 18 LEU A 9 -59.70 -144.82 REMARK 500 19 LYS A 8 -71.90 -160.45 REMARK 500 19 LEU A 9 -69.46 -148.02 REMARK 500 20 LYS A 8 -69.55 -161.22 REMARK 500 20 LEU A 9 -67.96 -144.23 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 A BETA3-SER ANALOGUE PEPTIDE REMARK 900 RELATED ID: 1J8Z RELATED DB: PDB REMARK 900 1J8Z CONTAINS A BETA3-CYS ANALOGUE PEPTIDE REMARK 900 RELATED ID: 1J9V RELATED DB: PDB REMARK 900 1J9V CONTAINS THE DABD LACTAM ANALOGUE PEPTIDE REMARK 900 RELATED ID: 1JAA RELATED DB: PDB REMARK 900 1JAA CONTAINS THE DAPE LACTAM ANALOGUE PEPTIDE. REMARK 900 RELATED ID: 1JAR RELATED DB: PDB REMARK 900 1JAR CONTAINS THE DDAB LACTAM ANALOGUE PEPTIDE DBREF 1JC8 A 2 14 UNP P12488 ENV_HV1BN 591 603 SEQADV 1JC8 ACE A 1 UNP P12488 ACETYLATION SEQADV 1JC8 ASP A 5 UNP P12488 CYS 594 ENGINEERED MUTATION SEQADV 1JC8 SET A 11 UNP P12488 CYS 600 ENGINEERED MUTATION SEQRES 1 A 14 ACE ILE TRP GLY ASP SER GLY LYS LEU ILE SET THR THR SEQRES 2 A 14 ALA MODRES 1JC8 SET A 11 SER AMINOSERINE HET ACE A 1 6 HET SET A 11 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 ILE A 10 N SET A 11 1555 1555 1.35 LINK CB SET A 11 N THR A 12 1555 1555 1.35 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 3.696 12.186 0.533 1.00 0.00 C HETATM 2 O ACE A 1 3.140 12.824 -0.363 1.00 0.00 O HETATM 3 CH3 ACE A 1 3.297 12.393 1.991 1.00 0.00 C HETATM 4 H1 ACE A 1 2.910 11.461 2.443 1.00 0.00 H HETATM 5 H2 ACE A 1 4.153 12.740 2.601 1.00 0.00 H HETATM 6 H3 ACE A 1 2.502 13.155 2.081 1.00 0.00 H