Header list of 1j8z.pdb file
Complete list - 27 20 Bytes
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 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 1 BCX A 5 CA - C - N ANGL. DEV. = 19.4 DEGREES
REMARK 500 2 BCX A 5 CA - C - N ANGL. DEV. = 19.7 DEGREES
REMARK 500 3 BCX A 5 CA - C - N ANGL. DEV. = 20.5 DEGREES
REMARK 500 5 BCX A 5 CA - C - N ANGL. DEV. = 19.0 DEGREES
REMARK 500 6 BCX A 5 CA - C - N ANGL. DEV. = 20.1 DEGREES
REMARK 500 7 BCX A 5 CA - C - N ANGL. DEV. = 17.2 DEGREES
REMARK 500 8 BCX A 5 CA - C - N ANGL. DEV. = 19.5 DEGREES
REMARK 500 9 BCX A 5 CA - C - N ANGL. DEV. = 18.6 DEGREES
REMARK 500 10 BCX A 5 CA - C - N ANGL. DEV. = 31.1 DEGREES
REMARK 500 11 BCX A 5 CA - C - N ANGL. DEV. = 18.7 DEGREES
REMARK 500 14 BCX A 5 CA - C - N ANGL. DEV. = 18.9 DEGREES
REMARK 500 15 BCX A 5 CA - C - N ANGL. DEV. = 18.8 DEGREES
REMARK 500 16 BCX A 5 CA - C - N ANGL. DEV. = 18.6 DEGREES
REMARK 500 17 BCX A 5 CA - C - N ANGL. DEV. = 30.6 DEGREES
REMARK 500 18 BCX A 5 CA - C - N ANGL. DEV. = 17.6 DEGREES
REMARK 500 19 BCX A 5 CA - C - N ANGL. DEV. = 18.3 DEGREES
REMARK 500 20 BCX A 5 CA - C - N ANGL. DEV. = 19.1 DEGREES
REMARK 500 21 BCX A 5 CA - C - N ANGL. DEV. = 16.9 DEGREES
REMARK 500 22 BCX A 5 CA - C - N ANGL. DEV. = 18.0 DEGREES
REMARK 500 23 BCX A 5 CA - C - N ANGL. DEV. = 19.6 DEGREES
REMARK 500 24 BCX A 5 CA - C - N ANGL. DEV. = 17.6 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 -75.79 -105.79
REMARK 500 1 LEU A 9 113.00 -160.14
REMARK 500 2 BCX A 5 -80.54 -129.51
REMARK 500 3 BCX A 5 -80.69 -128.54
REMARK 500 4 BCX A 5 -86.66 -124.71
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 -87.47 -89.82
REMARK 500 5 LEU A 9 116.44 -167.29
REMARK 500 6 BCX A 5 -83.91 -96.33
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 -79.90 -113.80
REMARK 500 7 LEU A 9 117.28 -165.12
REMARK 500 8 BCX A 5 -79.07 -108.00
REMARK 500 9 BCX A 5 -87.32 -138.79
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 11 BCX A 5 -91.68 -100.84
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 -96.68 -98.17
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 -95.07 -102.84
REMARK 500 13 SER A 6 84.04 -67.56
REMARK 500 14 BCX A 5 -67.73 -92.68
REMARK 500 15 BCX A 5 -82.71 -104.16
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 -79.56 -105.42
REMARK 500 16 LYS A 8 -70.93 -77.80
REMARK 500 17 TRP A 3 88.78 -150.78
REMARK 500 18 BCX A 5 -82.86 -116.51
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 -81.25 -91.28
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 -91.13 -95.18
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 -79.36 -131.55
REMARK 500 21 LEU A 9 117.82 -167.04
REMARK 500 22 BCX A 5 -84.67 -100.35
REMARK 500 22 LYS A 8 -70.81 -74.90
REMARK 500 22 LEU A 9 117.88 -169.08
REMARK 500
REMARK 500 THIS ENTRY HAS 54 RAMACHANDRAN OUTLIERS.
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 BCX A 5 12.53
REMARK 500 2 BCX A 5 12.64
REMARK 500 3 BCX A 5 12.15
REMARK 500 4 BCX A 5 13.88
REMARK 500 5 BCX A 5 12.75
REMARK 500 6 BCX A 5 12.61
REMARK 500 7 BCX A 5 12.11
REMARK 500 8 BCX A 5 12.50
REMARK 500 9 BCX A 5 12.73
REMARK 500 11 BCX A 5 12.79
REMARK 500 12 BCX A 5 14.02
REMARK 500 13 BCX A 5 13.93
REMARK 500 14 BCX A 5 12.13
REMARK 500 15 BCX A 5 12.25
REMARK 500 16 BCX A 5 12.25
REMARK 500 18 BCX A 5 12.62
REMARK 500 19 BCX A 5 12.90
REMARK 500 20 BCX A 5 11.97
REMARK 500 21 BCX A 5 12.46
REMARK 500 22 BCX A 5 12.76
REMARK 500 23 BCX A 5 12.53
REMARK 500 24 BCX A 5 12.64
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
Complete list - 27 20 Bytes