Header list of 1j8n.pdb file
Complete list - 27 20 Bytes
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 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 1 B3S A 6 C - N - CA ANGL. DEV. = 26.6 DEGREES
REMARK 500 2 B3S A 6 C - N - CA ANGL. DEV. = -15.1 DEGREES
REMARK 500 3 B3S A 6 C - N - CA ANGL. DEV. = -24.4 DEGREES
REMARK 500 4 B3S A 6 C - N - CA ANGL. DEV. = 21.2 DEGREES
REMARK 500 6 B3S A 6 C - N - CA ANGL. DEV. = 30.3 DEGREES
REMARK 500 8 B3S A 6 C - N - CA ANGL. DEV. = 30.4 DEGREES
REMARK 500 9 B3S A 6 C - N - CA ANGL. DEV. = 25.1 DEGREES
REMARK 500 11 B3S A 6 C - N - CA ANGL. DEV. = 29.9 DEGREES
REMARK 500 13 B3S A 6 C - N - CA ANGL. DEV. = 34.7 DEGREES
REMARK 500 14 B3S A 6 C - N - CA ANGL. DEV. = 34.9 DEGREES
REMARK 500 16 B3S A 6 C - N - CA ANGL. DEV. = 32.7 DEGREES
REMARK 500 24 B3S A 6 C - N - CA ANGL. DEV. = 20.3 DEGREES
REMARK 500 27 B3S A 6 C - N - CA ANGL. DEV. = 34.7 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 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 14.52 -116.14
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 B3S A 6 1.64 -94.52
REMARK 500 3 LEU A 9 -43.57 -165.02
REMARK 500 3 THR A 13 -81.66 -162.73
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 -8.28 -23.13
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 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 22.79 -112.92
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 -28.67 -42.94
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 LEU A 9 -45.18 -130.78
REMARK 500 9 ILE A 10 113.80 -165.21
REMARK 500 10 B3S A 6 15.77 -118.05
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 -29.29 -40.12
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 28.72 -114.30
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 57.30 -132.84
REMARK 500 13 LYS A 8 51.84 -95.90
REMARK 500 13 LEU A 9 -42.86 -166.12
REMARK 500 13 ILE A 10 112.94 -165.63
REMARK 500
REMARK 500 THIS ENTRY HAS 106 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 CYS A 5 B3S A 6 1 132.48
REMARK 500 CYS A 5 B3S A 6 2 135.18
REMARK 500 CYS A 5 B3S A 6 3 143.61
REMARK 500 CYS A 5 B3S A 6 4 128.72
REMARK 500 CYS A 5 B3S A 6 5 126.26
REMARK 500 CYS A 5 B3S A 6 6 137.54
REMARK 500 CYS A 5 B3S A 6 7 133.42
REMARK 500 CYS A 5 B3S A 6 8 137.64
REMARK 500 CYS A 5 B3S A 6 9 131.07
REMARK 500 CYS A 5 B3S A 6 10 134.42
REMARK 500 CYS A 5 B3S A 6 11 136.98
REMARK 500 CYS A 5 B3S A 6 12 130.76
REMARK 500 CYS A 5 B3S A 6 13 148.67
REMARK 500 CYS A 5 B3S A 6 14 149.50
REMARK 500 CYS A 5 B3S A 6 15 132.02
REMARK 500 CYS A 5 B3S A 6 16 142.24
REMARK 500 CYS A 5 B3S A 6 17 131.60
REMARK 500 CYS A 5 B3S A 6 18 132.72
REMARK 500 CYS A 5 B3S A 6 19 127.29
REMARK 500 CYS A 5 B3S A 6 20 129.53
REMARK 500 CYS A 5 B3S A 6 21 132.97
REMARK 500 CYS A 5 B3S A 6 22 134.20
REMARK 500 CYS A 5 B3S A 6 23 130.20
REMARK 500 CYS A 5 B3S A 6 24 128.19
REMARK 500 CYS A 5 B3S A 6 25 132.99
REMARK 500 CYS A 5 B3S A 6 26 127.69
REMARK 500 CYS A 5 B3S A 6 27 148.75
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
Complete list - 27 20 Bytes