HEADER VIRAL PROTEIN 22-MAY-01 1J8N TITLE SOLUTION STRUCTURE OF BETA3-ANALOGUE PEPTIDE CORRESPONDING TO THE GP41 TITLE 2 600-612 LOOP OF HIV. COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIV1 GP41 HSER ANALOGUE PEPTIDE ACE-ILE-TRP-GLY-CYS- COMPND 3 BETA3SER-GLY-LYS-LEU-ILE-CYS-THR-THR-ALA; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE PARENT SEQUENCE IWGCSGKLICTTA OCCURS IN HIV GP41 SOURCE 4 PROTEIN. THIS ANALOGUE CONTAINS A MODIFIED RESIDUE BSE WHICH IS A SOURCE 5 BETA3-SER (I.E. WITH AN ADDITIONAL CH2 BETWEEN NH AND CALPHA). KEYWDS BETA PEPTIDE, GP41, CYCLIC PEPTIDE, VIRAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 27 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 6 15-NOV-23 1J8N 1 ATOM REVDAT 5 27-OCT-21 1J8N 1 REMARK SEQADV REVDAT 4 24-JUN-20 1J8N 1 REMARK SEQADV LINK REVDAT 3 05-OCT-11 1J8N 1 REVDAT 2 24-FEB-09 1J8N 1 VERSN REVDAT 1 01-JUL-03 1J8N 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., WUETHRICH K. (DYANA), MOLECULAR SIMULATION REMARK 3 INC., SAN DIEGO (DISCOVER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 50 INITIAL RANDOM STRUCTURES WERE REMARK 3 CALCULATED USING SIMULATED ANNEALING IN DYANA SOFTWARE. REMARK 3 REFINEMENT WAS DONE WITH 500 STEPS RESTRAINED MINIMIZATION, 35PS REMARK 3 MD IN VACUO AT 300K FOR EQUILIBRATION, 200PS MD UNDER NMR REMARK 3 RESTRAINTS, AND 750PS CONJUGATED GRADIENT EM USING DISCOVER REMARK 3 MODULE OF MSI SOFTWARE. REMARK 4 REMARK 4 1J8N COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-MAY-01. REMARK 100 THE DEPOSITION ID IS D_1000013497. 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 : 2MM PEPTIDE ; 500UL DMSO-D6; 4MM REMARK 210 PEPTIDE ; 500UL DMSO-D6 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY 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 : 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 : 27 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. NOESY EXPERIMENTS WITH MIXING TIMES FROM REMARK 210 80MS TO 800MS WERE RECORDED IN ORDER TO DEFINE THE BEST REMARK 210 CONDITIONS IN ORDER TO AVOID 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: 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 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 2 B3S A 6 CA - C - N ANGL. DEV. = -22.7 DEGREES REMARK 500 3 B3S A 6 CA - C - N ANGL. DEV. = -27.4 DEGREES REMARK 500 5 B3S A 6 CA - C - N ANGL. DEV. = -24.0 DEGREES REMARK 500 7 B3S A 6 CA - C - N ANGL. DEV. = -20.8 DEGREES REMARK 500 8 B3S A 6 CA - C - N ANGL. DEV. = -14.7 DEGREES REMARK 500 9 B3S A 6 CA - C - N ANGL. DEV. = -15.4 DEGREES REMARK 500 10 B3S A 6 CA - C - N ANGL. DEV. = -22.2 DEGREES REMARK 500 11 B3S A 6 CA - C - N ANGL. DEV. = -14.4 DEGREES REMARK 500 12 B3S A 6 CA - C - N ANGL. DEV. = -19.3 DEGREES REMARK 500 13 B3S A 6 CA - C - N ANGL. DEV. = -22.4 DEGREES REMARK 500 15 B3S A 6 CA - C - N ANGL. DEV. = -16.4 DEGREES REMARK 500 16 B3S A 6 CA - C - N ANGL. DEV. = -20.9 DEGREES REMARK 500 17 B3S A 6 CA - C - N ANGL. DEV. = -21.2 DEGREES REMARK 500 18 B3S A 6 CA - C - N ANGL. DEV. = -20.5 DEGREES REMARK 500 19 B3S A 6 CA - C - N ANGL. DEV. = -13.4 DEGREES REMARK 500 20 B3S A 6 CA - C - N ANGL. DEV. = -14.1 DEGREES REMARK 500 21 B3S A 6 CA - C - N ANGL. DEV. = -18.4 DEGREES REMARK 500 23 B3S A 6 CA - C - N ANGL. DEV. = -29.1 DEGREES REMARK 500 25 B3S A 6 CA - C - N ANGL. DEV. = -21.6 DEGREES REMARK 500 26 B3S A 6 CA - C - N ANGL. DEV. = -21.7 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 B3S A 6 -3.42 -114.89 REMARK 500 1 LYS A 8 41.23 -90.16 REMARK 500 1 LEU A 9 -65.56 -107.17 REMARK 500 1 ILE A 10 81.47 -151.41 REMARK 500 1 THR A 13 89.27 -165.06 REMARK 500 2 B3S A 6 -22.54 -101.74 REMARK 500 2 LEU A 9 -43.02 -165.29 REMARK 500 2 THR A 12 116.35 -163.75 REMARK 500 2 THR A 13 101.07 -165.13 REMARK 500 3 LEU A 9 -43.57 -165.02 REMARK 500 3 THR A 13 -81.66 -162.73 REMARK 500 4 B3S A 6 -5.80 -106.95 REMARK 500 4 LYS A 8 66.68 -68.70 REMARK 500 4 LEU A 9 -43.51 -165.05 REMARK 500 4 THR A 13 -78.22 -157.45 REMARK 500 5 B3S A 6 33.15 -86.15 REMARK 500 5 LYS A 8 66.60 -69.00 REMARK 500 5 LEU A 9 -46.30 -153.60 REMARK 500 5 THR A 13 107.66 -165.11 REMARK 500 6 B3S A 6 -3.40 -122.41 REMARK 500 6 LYS A 8 40.23 -90.57 REMARK 500 6 LEU A 9 -68.15 -108.44 REMARK 500 6 ILE A 10 110.31 -166.06 REMARK 500 6 THR A 13 -79.86 -162.14 REMARK 500 7 B3S A 6 -10.50 -104.84 REMARK 500 7 LEU A 9 -43.04 -165.37 REMARK 500 7 THR A 13 -83.19 -162.42 REMARK 500 8 B3S A 6 33.89 -120.01 REMARK 500 8 LYS A 8 63.82 -69.10 REMARK 500 8 LEU A 9 -45.07 -132.75 REMARK 500 8 ILE A 10 114.18 -165.12 REMARK 500 8 THR A 13 110.65 -165.13 REMARK 500 9 B3S A 6 14.40 -111.56 REMARK 500 9 LEU A 9 -45.18 -130.78 REMARK 500 9 ILE A 10 113.80 -165.21 REMARK 500 10 B3S A 6 -21.76 -104.11 REMARK 500 10 LEU A 9 -42.33 -165.54 REMARK 500 10 ILE A 10 112.76 -162.95 REMARK 500 10 THR A 13 106.55 -165.15 REMARK 500 11 B3S A 6 34.79 -119.04 REMARK 500 11 LYS A 8 66.26 -68.66 REMARK 500 11 LEU A 9 -45.34 -136.13 REMARK 500 11 ILE A 10 114.25 -165.08 REMARK 500 11 THR A 13 -78.21 -157.41 REMARK 500 12 TRP A 3 96.82 -160.08 REMARK 500 12 B3S A 6 -2.19 -112.03 REMARK 500 12 LEU A 9 -42.50 -165.75 REMARK 500 12 ILE A 10 114.92 -165.05 REMARK 500 12 THR A 13 -85.78 -161.94 REMARK 500 13 B3S A 6 57.24 -156.51 REMARK 500 REMARK 500 THIS ENTRY HAS 110 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 B3S A 6 GLY A 7 1 144.55 REMARK 500 B3S A 6 GLY A 7 4 145.68 REMARK 500 B3S A 6 GLY A 7 6 144.37 REMARK 500 B3S A 6 GLY A 7 8 149.10 REMARK 500 B3S A 6 GLY A 7 9 149.54 REMARK 500 B3S A 6 GLY A 7 11 148.97 REMARK 500 B3S A 6 GLY A 7 14 145.32 REMARK 500 B3S A 6 GLY A 7 19 -149.73 REMARK 500 B3S A 6 GLY A 7 22 143.26 REMARK 500 B3S A 6 GLY A 7 24 144.59 REMARK 500 B3S A 6 GLY A 7 27 145.74 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 1 B3S A 6 -16.02 REMARK 500 4 B3S A 6 -15.32 REMARK 500 6 B3S A 6 -16.10 REMARK 500 7 B3S A 6 10.74 REMARK 500 8 B3S A 6 -13.62 REMARK 500 9 B3S A 6 -13.41 REMARK 500 10 B3S A 6 10.13 REMARK 500 11 B3S A 6 -13.68 REMARK 500 12 B3S A 6 11.36 REMARK 500 13 B3S A 6 10.05 REMARK 500 14 B3S A 6 -15.57 REMARK 500 15 B3S A 6 12.50 REMARK 500 16 B3S A 6 -11.36 REMARK 500 17 B3S A 6 10.63 REMARK 500 18 B3S A 6 10.95 REMARK 500 19 B3S A 6 13.42 REMARK 500 20 B3S A 6 13.17 REMARK 500 21 B3S A 6 11.78 REMARK 500 22 B3S A 6 -16.93 REMARK 500 24 B3S A 6 -15.96 REMARK 500 25 B3S A 6 10.41 REMARK 500 26 B3S A 6 -10.99 REMARK 500 27 B3S A 6 -15.29 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 1IM7 ENTRY CONTAINS THE PARENT PEPTIDE COORDINATES. DBREF 1J8N A 2 14 UNP P12488 ENV_HV1BN 591 603 SEQADV 1J8N ACE A 1 UNP P12488 ACETYLATION SEQADV 1J8N B3S A 6 UNP P12488 SER 595 ENGINEERED MUTATION SEQRES 1 A 14 ACE ILE TRP GLY CYS B3S GLY LYS LEU ILE CYS THR THR SEQRES 2 A 14 ALA HET ACE A 1 6 HET B3S A 6 13 HETNAM ACE ACETYL GROUP HETNAM B3S (3R)-3-AMINO-4-HYDROXYBUTANOIC ACID FORMUL 1 ACE C2 H4 O FORMUL 1 B3S C4 H9 N O3 SSBOND 1 CYS A 5 CYS A 11 1555 1555 2.10 LINK C ACE A 1 N ILE A 2 1555 1555 1.33 LINK C CYS A 5 N B3S A 6 1555 1555 1.34 LINK C B3S A 6 N GLY A 7 1555 1555 1.33 SITE 1 AC1 2 ILE A 2 B3S A 6 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 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 -6.759 3.224 5.513 1.00 0.00 C HETATM 2 O ACE A 1 -5.677 3.363 6.082 1.00 0.00 O HETATM 3 CH3 ACE A 1 -7.493 4.408 4.983 1.00 0.00 C HETATM 4 H1 ACE A 1 -6.796 5.063 4.460 1.00 0.00 H HETATM 5 H2 ACE A 1 -8.268 4.076 4.293 1.00 0.00 H HETATM 6 H3 ACE A 1 -7.950 4.951 5.810 1.00 0.00 H