HEADER VIRAL PROTEIN 23-MAY-01 1J8Z TITLE SOLUTION STRUCTURE OF BETA3 ANALOGUE PEPTIDE (HCYS) OF HIV GP41 600- TITLE 2 612 LOOP. COMPND MOL_ID: 1; COMPND 2 MOLECULE: HCYS BETA3-CYS 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 SEQUENCE IWGCSGKLICTTA OCCURS IN SOURCE 4 HIV GP41 GLYCOPROTEIN. THIS ANALOGUE CONTAINS A MODIFIED RESIDUE BCY SOURCE 5 WHICH IS A BETA3-CYS (I.E. WHITH AN ADDITIONAL CH2 BETWEEN NH AND SOURCE 6 CALPHA) KEYWDS BETA-PEPTIDE, GP41, CYCLIC PEPTIDE, VIRAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 24 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 4 15-NOV-23 1J8Z 1 ATOM REVDAT 3 27-OCT-21 1J8Z 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 1J8Z 1 VERSN REVDAT 1 01-JUL-03 1J8Z 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, DISCOVER 3 REMARK 3 AUTHORS : BRUKER GMBH (XWINNMR), MOLECULAR SIMULATION INC. , REMARK 3 SAN DIEGO (DISCOVER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 50 INITIAL RANDOM STRUCTURES WERE REMARK 3 GENERATED USING SIMULATED ANNEALING IN DYANA SOFTWARE, FOLLOWED REMARK 3 USING THE DISCOVER MODULE OF MSI SOFTWARE, BY 500 STEPS REMARK 3 RESTRAINED MINIMIZATION, 35 PS MD IN VACUO AT 300K, 200PS MD REMARK 3 UNDER NMR RESTRAINTS AND 750PS CONJUGATED GRADIENT EM. REMARK 4 REMARK 4 1J8Z 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_1000013509. 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 IN 500UL DMSO-D6; REMARK 210 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, DYANA REMARK 210 1.5, DISCOVER 3 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 : 24 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 WERE RECORDED WITH REMARK 210 MIXING TIMES FROM 80MS TO 800MS IN ORDER TO DETERMINED THE BEST REMARK 210 CONDITIONS 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: 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 0.143 REMARK 500 3 ALA A 14 C ALA A 14 OXT 0.141 REMARK 500 4 ALA A 14 C ALA A 14 OXT 0.142 REMARK 500 5 ALA A 14 C ALA A 14 OXT 0.145 REMARK 500 6 ALA A 14 C ALA A 14 OXT 0.142 REMARK 500 7 ALA A 14 C ALA A 14 OXT 0.143 REMARK 500 8 ALA A 14 C ALA A 14 OXT 0.144 REMARK 500 9 ALA A 14 C ALA A 14 OXT 0.144 REMARK 500 10 ALA A 14 C ALA A 14 OXT 0.146 REMARK 500 11 ALA A 14 C ALA A 14 OXT 0.142 REMARK 500 12 ALA A 14 C ALA A 14 OXT 0.144 REMARK 500 13 ALA A 14 C ALA A 14 OXT 0.141 REMARK 500 14 ALA A 14 C ALA A 14 OXT 0.143 REMARK 500 15 ALA A 14 C ALA A 14 OXT 0.142 REMARK 500 16 ALA A 14 C ALA A 14 OXT 0.144 REMARK 500 17 ALA A 14 C ALA A 14 OXT 0.146 REMARK 500 18 ALA A 14 C ALA A 14 OXT 0.145 REMARK 500 19 ALA A 14 C ALA A 14 OXT 0.145 REMARK 500 20 ALA A 14 C ALA A 14 OXT 0.146 REMARK 500 21 ALA A 14 C ALA A 14 OXT 0.144 REMARK 500 22 ALA A 14 C ALA A 14 OXT 0.144 REMARK 500 23 ALA A 14 C ALA A 14 OXT 0.142 REMARK 500 24 ALA A 14 C ALA A 14 OXT 0.142 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 BCX A 5 C - N - CA ANGL. DEV. = 23.8 DEGREES REMARK 500 3 BCX A 5 C - N - CA ANGL. DEV. = 23.5 DEGREES REMARK 500 4 BCX A 5 C - N - CA ANGL. DEV. = 17.0 DEGREES REMARK 500 9 BCX A 5 C - N - CA ANGL. DEV. = 29.9 DEGREES REMARK 500 18 BCX A 5 C - N - CA ANGL. DEV. = 15.9 DEGREES REMARK 500 21 BCX A 5 C - N - CA ANGL. DEV. = 23.6 DEGREES REMARK 500 24 BCX A 5 C - N - CA ANGL. DEV. = 16.9 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 BCX A 5 150.81 73.25 REMARK 500 1 LEU A 9 113.00 -160.14 REMARK 500 2 BCX A 5 153.14 42.65 REMARK 500 3 BCX A 5 156.46 39.44 REMARK 500 4 BCX A 5 124.48 72.45 REMARK 500 4 SER A 6 87.99 -59.53 REMARK 500 4 LYS A 8 -71.16 -79.03 REMARK 500 4 ILE A 10 142.14 -33.28 REMARK 500 5 BCX A 5 154.56 70.70 REMARK 500 5 LEU A 9 116.44 -167.29 REMARK 500 6 BCX A 5 153.32 68.92 REMARK 500 6 LEU A 9 110.04 -162.65 REMARK 500 7 TRP A 3 -64.67 -159.10 REMARK 500 7 BCX A 5 147.96 66.55 REMARK 500 7 LEU A 9 117.28 -165.12 REMARK 500 8 BCX A 5 152.66 67.01 REMARK 500 9 BCX A 5 153.73 24.40 REMARK 500 9 LYS A 8 -71.83 -77.18 REMARK 500 9 LEU A 9 107.55 -160.85 REMARK 500 9 THR A 12 -65.74 -148.09 REMARK 500 10 BCX A 5 -175.77 90.92 REMARK 500 11 BCX A 5 155.68 58.43 REMARK 500 11 ILE A 10 103.74 -46.45 REMARK 500 11 CYS A 11 58.24 -150.05 REMARK 500 12 BCX A 5 127.39 81.46 REMARK 500 12 SER A 6 83.57 -67.95 REMARK 500 12 THR A 12 -36.28 -154.95 REMARK 500 13 BCX A 5 126.68 80.32 REMARK 500 13 SER A 6 84.04 -67.56 REMARK 500 14 BCX A 5 144.79 95.42 REMARK 500 15 BCX A 5 153.20 66.57 REMARK 500 15 ILE A 10 109.15 -55.46 REMARK 500 15 CYS A 11 64.65 -106.43 REMARK 500 16 TRP A 3 -101.38 -146.67 REMARK 500 16 BCX A 5 152.58 70.19 REMARK 500 16 LYS A 8 -70.93 -77.80 REMARK 500 17 TRP A 3 88.78 -150.78 REMARK 500 17 BCX A 5 -179.98 78.81 REMARK 500 18 BCX A 5 148.72 59.61 REMARK 500 18 LYS A 8 -70.74 -75.79 REMARK 500 18 LEU A 9 116.54 -166.51 REMARK 500 19 BCX A 5 148.89 80.37 REMARK 500 19 LEU A 9 117.39 -166.08 REMARK 500 20 TRP A 3 -31.28 -166.35 REMARK 500 20 BCX A 5 161.17 59.11 REMARK 500 20 ILE A 10 102.77 -50.47 REMARK 500 20 CYS A 11 52.80 -148.42 REMARK 500 21 BCX A 5 146.58 51.37 REMARK 500 21 LEU A 9 117.82 -167.04 REMARK 500 22 BCX A 5 150.22 69.79 REMARK 500 REMARK 500 THIS ENTRY HAS 56 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 GLY A 4 BCX A 5 1 136.32 REMARK 500 GLY A 4 BCX A 5 2 143.11 REMARK 500 GLY A 4 BCX A 5 3 143.17 REMARK 500 GLY A 4 BCX A 5 4 133.59 REMARK 500 BCX A 5 SER A 6 4 148.28 REMARK 500 GLY A 4 BCX A 5 5 139.83 REMARK 500 GLY A 4 BCX A 5 6 144.43 REMARK 500 GLY A 4 BCX A 5 7 135.11 REMARK 500 BCX A 5 SER A 6 7 149.67 REMARK 500 GLY A 4 BCX A 5 8 135.24 REMARK 500 GLY A 4 BCX A 5 9 146.65 REMARK 500 GLY A 4 BCX A 5 10 145.93 REMARK 500 GLY A 4 BCX A 5 11 136.89 REMARK 500 BCX A 5 SER A 6 11 149.60 REMARK 500 GLY A 4 BCX A 5 12 133.81 REMARK 500 BCX A 5 SER A 6 12 146.93 REMARK 500 GLY A 4 BCX A 5 13 133.34 REMARK 500 BCX A 5 SER A 6 13 146.63 REMARK 500 GLY A 4 BCX A 5 14 141.35 REMARK 500 GLY A 4 BCX A 5 15 134.16 REMARK 500 GLY A 4 BCX A 5 16 131.43 REMARK 500 GLY A 4 BCX A 5 17 144.98 REMARK 500 GLY A 4 BCX A 5 18 138.52 REMARK 500 BCX A 5 SER A 6 18 149.78 REMARK 500 GLY A 4 BCX A 5 19 141.50 REMARK 500 GLY A 4 BCX A 5 20 130.10 REMARK 500 GLY A 4 BCX A 5 21 138.33 REMARK 500 BCX A 5 SER A 6 21 149.87 REMARK 500 GLY A 4 BCX A 5 22 139.53 REMARK 500 BCX A 5 SER A 6 22 149.75 REMARK 500 GLY A 4 BCX A 5 23 140.32 REMARK 500 GLY A 4 BCX A 5 24 138.63 REMARK 500 BCX A 5 SER A 6 24 149.62 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 (HSER). DBREF 1J8Z A 2 14 UNP P12488 ENV_HV1BN 591 603 SEQADV 1J8Z ACE A 1 UNP P12488 ACETYLATION SEQADV 1J8Z BCX A 5 UNP P12488 CYS 594 ENGINEERED MUTATION SEQRES 1 A 14 ACE ILE TRP GLY BCX SER GLY LYS LEU ILE CYS THR THR SEQRES 2 A 14 ALA MODRES 1J8Z BCX A 5 CYS BETA-3-CYSTEINE HET ACE A 1 6 HET BCX A 5 13 HETNAM ACE ACETYL GROUP HETNAM BCX (3R)-3-AMINO-4-SULFANYLBUTANOIC ACID FORMUL 1 ACE C2 H4 O FORMUL 1 BCX C4 H9 N O2 S LINK C ACE A 1 N ILE A 2 1555 1555 1.34 LINK C GLY A 4 N BCX A 5 1555 1555 1.34 LINK C BCX A 5 N SER A 6 1555 1555 1.33 LINK SG BCX A 5 SG CYS A 11 1555 1555 2.00 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 -8.162 -4.739 -4.997 1.00 0.00 C HETATM 2 O ACE A 1 -8.180 -3.509 -5.072 1.00 0.00 O HETATM 3 CH3 ACE A 1 -7.831 -5.586 -6.222 1.00 0.00 C HETATM 4 H1 ACE A 1 -7.636 -4.948 -7.103 1.00 0.00 H HETATM 5 H2 ACE A 1 -6.926 -6.199 -6.056 1.00 0.00 H HETATM 6 H3 ACE A 1 -8.664 -6.264 -6.485 1.00 0.00 H