Header list of 1jd8.pdb file
Complete list - 10 20 Bytes
HEADER VIRAL PROTEIN 13-JUN-01 1JD8
TITLE SOLUTION STRUCTURE OF LACTAM ANALOGUE DAPD OF HIV GP41 600-612 LOOP
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: TRANSMEMBRANE PROTEIN GP41;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: TM, GLYCOPROTEIN 41, GP41;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1;
SOURCE 4 ORGANISM_TAXID: 11676;
SOURCE 5 OTHER_DETAILS: THE PARENT PEPTIDE (IWGCSGKLICTTA) OCCURS NATURALLY
SOURCE 6 IN HIV GP41
KEYWDS CYCLIC PEPTIDE, GP41, HIV, LACTAM BOND, PSEUDOPEPTIDE, VIRAL 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 5 10-OCT-18 1JD8 1 TITLE CAVEAT COMPND SOURCE
REVDAT 5 2 1 REMARK DBREF SEQADV SEQRES
REVDAT 5 3 1 HET HETNAM FORMUL LINK
REVDAT 5 4 1 CRYST1 ATOM
REVDAT 4 03-OCT-18 1JD8 1 CAVEAT REMARK
REVDAT 3 24-FEB-09 1JD8 1 VERSN
REVDAT 2 25-MAY-04 1JD8 1 CHNID HET
REVDAT 1 01-JUL-03 1JD8 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 : DYANA 1.5, DISCOVER 3
REMARK 3 AUTHORS : GUENTERT P., MUMENTHALER C. AND WUETHRICH K.
REMARK 3 (1997) J. MOL. BIOL., 273,283-298 (DYANA), MSI,
REMARK 3 SAN DIEGO (DISCOVER)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: 50 INITIAL STRUCTURES WERE GENERATED
REMARK 3 USING DYANA SOFTWARE, FOLLOWED BY 500 STEPS RESTRAINED
REMARK 3 MINIMIZATION.THEN USING DISCOVER 3, 35 PS MD AND 750 STEPS
REMARK 3 CONJUGATE GRADIENT EM.
REMARK 4
REMARK 4 1JD8 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_1000013646.
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 : 4MM PEPTIDE IN 500 UL 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 DYNAMICS, MOLECULAR
REMARK 210 DYNAMICS, ENERGY MINIMIZATION
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 50
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST
REMARK 210 ENERGY
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK: CLASSICAL 2D HOMONUCLEAR NMR TECHNQUES WERE USED.
REMARK 210 DIFFERENT NOESY WITH DIFFERENT MIXING TIME (FROM 80MS TO 800MS)
REMARK 210 WERE RECORDED IN ORDER TO DETERMINE THE BEST CONDITIONS WITHOUT
REMARK 210 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 0.142
REMARK 500 3 ALA A 14 C ALA A 14 OXT 0.138
REMARK 500 4 ALA A 14 C ALA A 14 OXT 0.141
REMARK 500 5 ALA A 14 C ALA A 14 OXT 0.141
REMARK 500 6 ALA A 14 C ALA A 14 OXT 0.139
REMARK 500 7 ALA A 14 C ALA A 14 OXT 0.145
REMARK 500 8 ALA A 14 C ALA A 14 OXT 0.141
REMARK 500 9 ALA A 14 C ALA A 14 OXT 0.140
REMARK 500 10 ALA A 14 C ALA A 14 OXT 0.145
REMARK 500 11 ALA A 14 C ALA A 14 OXT 0.145
REMARK 500 12 ALA A 14 C ALA A 14 OXT 0.141
REMARK 500 13 ALA A 14 C ALA A 14 OXT 0.143
REMARK 500 14 ALA A 14 C ALA A 14 OXT 0.141
REMARK 500 15 ALA A 14 C ALA A 14 OXT 0.141
REMARK 500 16 ALA A 14 C ALA A 14 OXT 0.141
REMARK 500 17 ALA A 14 C ALA A 14 OXT 0.145
REMARK 500 18 ALA A 14 C ALA A 14 OXT 0.141
REMARK 500 19 ALA A 14 C ALA A 14 OXT 0.140
REMARK 500 20 ALA A 14 C ALA A 14 OXT 0.143
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 SER A 6 115.19 -163.20
REMARK 500 1 LYS A 8 -84.61 -158.03
REMARK 500 1 THR A 13 79.82 -100.20
REMARK 500 2 SER A 6 119.04 -162.16
REMARK 500 2 LYS A 8 -85.88 -152.98
REMARK 500 3 SER A 6 113.30 -162.34
REMARK 500 3 LYS A 8 -82.29 -160.73
REMARK 500 3 THR A 12 108.48 -56.00
REMARK 500 4 LYS A 8 -94.93 -153.47
REMARK 500 4 THR A 12 102.93 -57.84
REMARK 500 5 SER A 6 108.37 -162.14
REMARK 500 5 LYS A 8 -92.03 -154.53
REMARK 500 5 THR A 12 99.48 -69.39
REMARK 500 6 SER A 6 113.93 -166.22
REMARK 500 6 LYS A 8 -85.48 -158.46
REMARK 500 6 THR A 12 108.04 -56.88
REMARK 500 7 LYS A 8 -90.32 -159.91
REMARK 500 8 LYS A 8 -95.03 -159.90
REMARK 500 9 LYS A 8 -90.62 -155.06
REMARK 500 10 SER A 6 111.99 -162.62
REMARK 500 10 LYS A 8 -92.36 -150.87
REMARK 500 10 THR A 12 105.72 -59.46
REMARK 500 11 DPP A 5 82.64 -151.48
REMARK 500 11 SER A 6 113.24 -167.61
REMARK 500 11 LYS A 8 -90.85 -148.06
REMARK 500 12 LYS A 8 -85.81 -157.75
REMARK 500 12 THR A 13 -65.04 -93.43
REMARK 500 13 LYS A 8 -89.19 -155.57
REMARK 500 13 THR A 13 -69.42 -97.53
REMARK 500 14 LYS A 8 -89.53 -156.20
REMARK 500 14 THR A 13 -73.36 -130.65
REMARK 500 15 LYS A 8 -99.34 -156.30
REMARK 500 16 LYS A 8 -93.57 -152.49
REMARK 500 16 THR A 12 104.37 -58.51
REMARK 500 16 THR A 13 -72.72 -140.87
REMARK 500 17 LYS A 8 -91.36 -159.50
REMARK 500 18 LYS A 8 -91.65 -161.90
REMARK 500 19 LYS A 8 -94.38 -158.81
REMARK 500 19 THR A 13 -73.09 -142.33
REMARK 500 20 SER A 6 105.33 -161.00
REMARK 500 20 LYS A 8 -92.43 -154.29
REMARK 500 20 THR A 13 -77.08 -132.04
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 THE BETA3-SER ANALOGUE PEPTIDE (HSER)
REMARK 900 RELATED ID: 1J8Z RELATED DB: PDB
REMARK 900 1J8Z CONTAINS THE BETA3-CYS ANALOGUE PEPTIDE (HCYS)
REMARK 900 RELATED ID: 1J9V RELATED DB: PDB
REMARK 900 1J9V CONTAINS THE LACTAM ANALOGUE PEPTIDE DABD
REMARK 900 RELATED ID: 1JAR RELATED DB: PDB
REMARK 900 1JAR CONTAINS THE LACTAM ANALOGUE PEPTIDEV DDAB
REMARK 900 RELATED ID: 1JC8 RELATED DB: PDB
REMARK 900 1JC8 CONTAINS THE LACTAM ANALOGUE PEPTIDE DDAP
REMARK 900 RELATED ID: 1JAA RELATED DB: PDB
REMARK 900 1JAA CONTAINS THE LACTAM ANALOGUE PEPTIDE DAPE
REMARK 900 RELATED ID: 1JCP RELATED DB: PDB
REMARK 900 1JCP CONTAINS THE LACTAM ANALOGUE PEPTIDE EDAP
DBREF 1JD8 A 2 14 UNP P03377 ENV_HV1BR 600 612
SEQADV 1JD8 ACE A 1 UNP P03377 ACETYLATION
SEQADV 1JD8 DPP A 5 UNP P03377 CYS 603 ENGINEERED MUTATION
SEQADV 1JD8 ASP A 11 UNP P03377 CYS 609 ENGINEERED MUTATION
SEQRES 1 A 14 ACE ILE TRP GLY DPP SER GLY LYS LEU ILE ASP THR THR
SEQRES 2 A 14 ALA
MODRES 1JD8 DPP A 5 SER AMINOSERINE
HET ACE A 1 6
HET DPP A 5 11
HETNAM ACE ACETYL GROUP
HETNAM DPP DIAMINOPROPANOIC ACID
FORMUL 1 ACE C2 H4 O
FORMUL 1 DPP C3 H8 N2 O2
LINK C ACE A 1 N ILE A 2 1555 1555 1.34
LINK C GLY A 4 N DPP A 5 1555 1555 1.35
LINK C DPP A 5 N SER A 6 1555 1555 1.35
LINK NG DPP A 5 CG ASP A 11 1555 1555 1.34
CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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 - 10 20 Bytes