1CVQ - Header Asymmetric Unit

HEADER DNA BINDING PROTEIN 24-AUG-99 1CVQ

TITLE SOLUTION STRUCTURE OF THE ANALOGUE RETRO-INVERSO MGREGRIGGC TITLE 2 IN CONTACT WITH THE MONOCLONAL ANTIBODY MAB 4X11, NMR, 7 TITLE 3 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 SOURCE 4 SEQUENCE CGG WAS ADDED AS A LINKER TO THE DEXTRAN MATRIX SOURCE 5 IN BIACORE EXPERIMENTS VIA THE CYS THIOL GROUP. NH2-CO WAS SOURCE 6 ADDED AT THE C-TERMINAL EXTREMITY OF THE RETRO-INVERSO SOURCE 7 PEPTIDE IN ORDER TO MIMIC THE N-TERMINAL OF THE PARENT SOURCE 8 PEPTIDE. ALL NON GLYCINE RESIDUES PRESENT A D- SOURCE 9 CONFIGURATION EXCEPT CYS.

KEYWDS PSEUDOMIMETIC, SYNTHETIC PEPTIDE, RETRO-INVERSO ANALOGUE, KEYWDS 2 TR-NOE, 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, AUTHOR 2 M.T.CUNG

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, JRNL AUTH 2 S.MULLER,M.T.CUNG JRNL TITL STRUCTURE OF ANTIBODY-BOUND PEPTIDES AND JRNL TITL 2 RETRO-INVERSO ANALOGUES. A TRANSFERRED NUCLEAR JRNL TITL 3 OVERHAUSER EFFECT SPECTROSCOPY AND MOLECULAR JRNL TITL 4 DYNAMICS APPROACH. JRNL REF BIOCHEMISTRY V. 40 5720 2001 JRNL REFN ISSN 0006-2960 JRNL PMID 11341837 JRNL DOI 10.1021/BI001151H

REMARK 1

REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DISCOVER 3 REMARK 3 AUTHORS : MOLECULAR SIMULATIONS INC., SAN DIEGO, CA REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A SET OF REMARK 3 35 TO 60 BACKBONE-BACKBONE, BACKBONE-SIDE CHAIN AND SIDE CHAIN REMARK 3 -SIDE CHAIN DISTANCE RESTRAINTS. THE PHI ANGLE FOR THE NON REMARK 3 GLYCINE D-RESIDUES WAS CONSTRAINED BETWEEN 0 AND 175. A REMARK 3 DISTANCE DEPENDENT DIELECTRIC CONSTANT EQUAL TO 4R WAS REMARK 3 APPLIED. THE NET ELECTRIC CHARGES WERE DECREASED, WHILE THOSE REMARK 3 OF THE N AND C TERMINAL 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 26-AUG-99. REMARK 100 THE RCSB ID CODE IS RCSB009568.

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 REMARK 210 MM PHOSPHATE BUFFER CONTAINING REMARK 210 0.02% 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 : DYANA 1.4, DISCOVER 3, REMARK 210 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. REMARK 210 5 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 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 REMARK 900 IRGERA. REMARK 900 RELATED ID: 1CT6 RELATED DB: PDB REMARK 900 1CT6 IS THE PARENT PEPTIDE, AN ANALOGUE PEPTIDE OF THE REMARK 900 IRGERA 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

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