Header list of 1cvq.pdb file
Complete list - 16 202 Bytes
HEADER DNA BINDING PROTEIN 24-AUG-99 1CVQ
TITLE SOLUTION STRUCTURE OF THE ANALOGUE RETRO-INVERSO MGREGRIGGC IN CONTACT
TITLE 2 WITH THE MONOCLONAL ANTIBODY MAB 4X11, NMR, 7 STRUCTURES
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: HISTONE H3;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: C-TERMINAL DOMAIN 130-135;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE
SOURCE 4 CGG WAS ADDED AS A LINKER TO THE DEXTRAN MATRIX IN BIACORE
SOURCE 5 EXPERIMENTS VIA THE CYS THIOL GROUP. NH2-CO WAS ADDED AT THE C-
SOURCE 6 TERMINAL EXTREMITY OF THE RETRO-INVERSO PEPTIDE IN ORDER TO MIMIC
SOURCE 7 THE N-TERMINAL OF THE PARENT PEPTIDE. ALL NON GLYCINE RESIDUES
SOURCE 8 PRESENT A D-CONFIGURATION EXCEPT CYS.
KEYWDS PSEUDOMIMETIC, SYNTHETIC PEPTIDE, RETRO-INVERSO ANALOGUE, TR-NOE,
KEYWDS 2 ANTIGEN- ANTIBODY COMPLEX, DNA BINDING PROTEIN
EXPDTA SOLUTION NMR
NUMMDL 7
AUTHOR A.PHAN CHAN DU,M.C.PETIT,G.GUICHARD,J.P.BRIAND,S.MULLER,M.T.CUNG
REVDAT 6 16-FEB-22 1CVQ 1 REMARK LINK
REVDAT 5 24-FEB-09 1CVQ 1 VERSN
REVDAT 4 01-APR-03 1CVQ 1 JRNL
REVDAT 3 13-JUN-01 1CVQ 1 JRNL REMARK
REVDAT 2 28-JUN-00 1CVQ 1 SOURCE
REVDAT 1 02-SEP-99 1CVQ 0
JRNL AUTH A.PHAN-CHAN-DU,M.C.PETIT,G.GUICHARD,J.P.BRIAND,S.MULLER,
JRNL AUTH 2 M.T.CUNG
JRNL TITL STRUCTURE OF ANTIBODY-BOUND PEPTIDES AND RETRO-INVERSO
JRNL TITL 2 ANALOGUES. A TRANSFERRED NUCLEAR OVERHAUSER EFFECT
JRNL TITL 3 SPECTROSCOPY AND MOLECULAR DYNAMICS APPROACH.
JRNL REF BIOCHEMISTRY V. 40 5720 2001
JRNL REFN ISSN 0006-2960
JRNL PMID 11341837
JRNL DOI 10.1021/BI001151H
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : DYANA 1.4, DISCOVER 3
REMARK 3 AUTHORS : GUNTERT, WUTHRICH (DYANA), MOLECULAR SIMULATIONS
REMARK 3 INC., SAN DIEGO, CA (DISCOVER)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A SET OF 35
REMARK 3 TO 60 BACKBONE-BACKBONE, BACKBONE-SIDE CHAIN AND SIDE CHAIN-SIDE
REMARK 3 CHAIN DISTANCE RESTRAINTS. THE PHI ANGLE FOR THE NON GLYCINE D-
REMARK 3 RESIDUES WAS CONSTRAINED BETWEEN 0 AND 175. A DISTANCE DEPENDENT
REMARK 3 DIELECTRIC CONSTANT EQUAL TO 4R WAS APPLIED. THE NET ELECTRIC
REMARK 3 CHARGES WERE DECREASED, WHILE THOSE OF THE N AND C TERMINAL
REMARK 3 CHARGED GROUPS WERE NEGLECTED.
REMARK 4
REMARK 4 1CVQ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-AUG-99.
REMARK 100 THE DEPOSITION ID IS D_1000009568.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 277
REMARK 210 PH : 7
REMARK 210 IONIC STRENGTH : 0.1M PHOSPHATE
REMARK 210 PRESSURE : 1 ATM
REMARK 210 SAMPLE CONTENTS : 5 MM PEPTIDE, 0.1 MM MAB; 100 MM
REMARK 210 PHOSPHATE BUFFER CONTAINING 0.02%
REMARK 210 SODIUM AZIDE
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : COSY, TOCSY, NOESY
REMARK 210 SPECTROMETER FIELD STRENGTH : 400 MHZ
REMARK 210 SPECTROMETER MODEL : DRX
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : DISCOVER 3, XWINNMR 1.2
REMARK 210 METHOD USED : ENERGY MINIMISATION MOLECULAR
REMARK 210 DYNAMICS (SIMULATED ANNEALING)
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 50
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 7
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST
REMARK 210 ENERGY
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 7
REMARK 210
REMARK 210 REMARK: THE PEPTIDE/MAB MOLAR RATIO WAS ADJUSTED TO 50/1 (I.E. 5
REMARK 210 MM OF PEPTIDE AND 0.1 MM MAB).
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 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 DAR A 5 NE - CZ - NH2 ANGL. DEV. = 3.8 DEGREES
REMARK 500 2 DAR A 5 NE - CZ - NH2 ANGL. DEV. = 4.0 DEGREES
REMARK 500 3 DAR A 5 NE - CZ - NH2 ANGL. DEV. = 3.9 DEGREES
REMARK 500 4 DAR A 5 NE - CZ - NH2 ANGL. DEV. = 3.9 DEGREES
REMARK 500 5 DAR A 5 NE - CZ - NH2 ANGL. DEV. = 3.8 DEGREES
REMARK 500 6 DAR A 5 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES
REMARK 500 7 DAR A 5 NE - CZ - NH2 ANGL. DEV. = 3.8 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 DIL A 6 72.99 71.06
REMARK 500 5 DIL A 6 76.22 91.15
REMARK 500 6 DIL A 6 78.58 91.31
REMARK 500 7 DIL A 6 -65.70 102.80
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 NH2 A 10
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1CS9 RELATED DB: PDB
REMARK 900 1CS9 IS THE PARENT PEPTIDE OF THE ORIGINAL SEQUENCE OF IRGERA.
REMARK 900 RELATED ID: 1CT6 RELATED DB: PDB
REMARK 900 1CT6 IS THE PARENT PEPTIDE, AN ANALOGUE PEPTIDE OF THE IRGERA
REMARK 900 SEQUENCE. (IN THIS PEPTIDE, ALA WAS REPLACED BY GLY).
DBREF 1CVQ A 2 10 PDB 1CVQ 1CVQ 2 10
SEQRES 1 A 9 MGG DGL GLY DAR DIL GLY GLY CYS NH2
MODRES 1CVQ MGG A 2 ARG
MODRES 1CVQ DGL A 3 GLU D-GLUTAMIC ACID
MODRES 1CVQ DAR A 5 ARG D-ARGININE
MODRES 1CVQ DIL A 6 ILE D-ISOLEUCINE
HET MGG A 2 33
HET DGL A 3 15
HET DAR A 5 24
HET DIL A 6 19
HET NH2 A 10 3
HETNAM MGG 2-(2-CARBOXY-ACETYLAMINO)-5-GUANIDINO-PENTANOIC ACID
HETNAM DGL D-GLUTAMIC ACID
HETNAM DAR D-ARGININE
HETNAM DIL D-ISOLEUCINE
HETNAM NH2 AMINO GROUP
HETSYN MGG D-ARGININE WITH 3-OXO-PROPIONIC ACID MODIFICATION
FORMUL 1 MGG C9 H17 N4 O5 1+
FORMUL 1 DGL C5 H9 N O4
FORMUL 1 DAR C6 H15 N4 O2 1+
FORMUL 1 DIL C6 H13 N O2
FORMUL 1 NH2 H2 N
LINK C MGG A 2 N DGL A 3 1555 1555 1.36
LINK C DGL A 3 N GLY A 4 1555 1555 1.35
LINK C GLY A 4 N DAR A 5 1555 1555 1.35
LINK C DAR A 5 N DIL A 6 1555 1555 1.35
LINK C DIL A 6 N GLY A 7 1555 1555 1.34
LINK C CYS A 9 N NH2 A 10 1555 1555 1.33
SITE 1 AC1 1 CYS A 9
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 - 16 202 Bytes