HEADER DNA BINDING PROTEIN 26-AUG-99 1CW8 TITLE SOLUTION STRUCTURE OF THE ANALOGUE RETRO-INVERSO (MA-R)REGRIGGC IN TITLE 2 CONTACT WITH THE MONOCLONAL ANTIBODY MAB 4X11, NMR, 6 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. TWO RI(MA) DIASTEREISOMERS SOURCE 9 WERE OBTAINED AND COULDN'T BE SEPARATED. KEYWDS PSEUDOMIMETIC, SYNTHETIC PEPTIDE, RETRO-INVERSO ANALOGUE, TR-NOE, KEYWDS 2 ANTIGEN- ANTIBODY COMPLEX, DNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 6 AUTHOR A.PHAN CHAN DU,M.C.PETIT,G.GUICHARD,J.P.BRIAND,S.MULLER,T.CUNG REVDAT 5 16-FEB-22 1CW8 1 REMARK LINK REVDAT 4 24-FEB-09 1CW8 1 VERSN REVDAT 3 01-APR-03 1CW8 1 JRNL REVDAT 2 13-JUN-01 1CW8 1 JRNL REMARK FORMUL REVDAT 1 03-SEP-99 1CW8 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 1CW8 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 DEPOSITION ID IS D_1000009585. 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 CONTAINNING 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 : 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 : 6 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 5 REMARK 210 REMARK 210 REMARK: THE PEPTIDE/MAB MOLAR RATIO WAS ADJUSTED TO 50/1(I.E. 5 MM REMARK 210 OF PEPTIDE AND 0.1 MM OF 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 2 NE - CZ - NH2 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DAR A 5 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 DAR A 2 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 DAR A 5 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 3 DAR A 2 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 3 DAR A 5 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 4 DAR A 2 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 4 DAR A 5 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 5 DAR A 2 NE - CZ - NH2 ANGL. DEV. = 3.6 DEGREES REMARK 500 5 DAR A 5 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 6 DAR A 2 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 6 DAR A 5 NE - CZ - NH1 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 2 DIL A 6 -69.49 115.96 REMARK 500 3 DIL A 6 -70.71 153.26 REMARK 500 5 DIL A 6 73.07 85.06 REMARK 500 6 DIL A 6 -66.85 110.22 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 DXX A 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1CS9 RELATED DB: PDB REMARK 900 1CS9 IS THE PARENT PEPTIDE. REMARK 900 RELATED ID: 1CT6 RELATED DB: PDB REMARK 900 1CT6 IS A PARENT ANALOGUE PEPTIDE OF THE IRGERA SEQUENCE. (IN THIS REMARK 900 PEPTIDE, ALA WAS REPLACED BY GLY). REMARK 900 RELATED ID: 1CVQ RELATED DB: PDB REMARK 900 1 CVQ IS THE RETRO-INVERSO ANALOGUE OF 1CT6. DBREF 1CW8 A 2 10 PDB 1CW8 1CW8 2 10 SEQRES 1 A 9 DAR DGL GLY DAR DIL GLY GLY CYS NH2 MODRES 1CW8 DAR A 2 ARG D-ARGININE MODRES 1CW8 DGL A 3 GLU D-GLUTAMIC ACID MODRES 1CW8 DAR A 5 ARG D-ARGININE MODRES 1CW8 DIL A 6 ILE D-ISOLEUCINE HET DAR A 2 24 HET DGL A 3 15 HET DAR A 5 24 HET DIL A 6 19 HET NH2 A 10 3 HET DXX A 1 12 HETNAM DAR D-ARGININE HETNAM DGL D-GLUTAMIC ACID HETNAM DIL D-ISOLEUCINE HETNAM NH2 AMINO GROUP HETNAM DXX METHYLMALONIC ACID FORMUL 1 DAR 2(C6 H15 N4 O2 1+) FORMUL 1 DGL C5 H9 N O4 FORMUL 1 DIL C6 H13 N O2 FORMUL 1 NH2 H2 N FORMUL 2 DXX C4 H6 O4 LINK C DXX A 1 N DAR A 2 1555 1555 1.35 LINK C DAR 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 1.35 LINK C CYS A 9 N NH2 A 10 1555 1555 1.33 SITE 1 AC1 2 DAR A 2 DGL A 3 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 HETATM 1 N DAR A 2 1.521 -3.903 0.981 1.00 0.00 N HETATM 2 CA DAR A 2 1.545 -2.438 1.238 1.00 0.00 C HETATM 3 CB DAR A 2 0.099 -1.871 1.244 1.00 0.00 C HETATM 4 CG DAR A 2 -0.825 -2.307 2.406 1.00 0.00 C HETATM 5 CD DAR A 2 -2.171 -1.552 2.450 1.00 0.00 C HETATM 6 NE DAR A 2 -3.035 -1.844 1.274 1.00 0.00 N HETATM 7 CZ DAR A 2 -3.925 -0.986 0.739 1.00 0.00 C HETATM 8 NH1 DAR A 2 -4.575 -1.366 -0.344 1.00 0.00 N HETATM 9 NH2 DAR A 2 -4.189 0.221 1.233 1.00 0.00 N HETATM 10 C DAR A 2 2.422 -1.738 0.152 1.00 0.00 C HETATM 11 O DAR A 2 1.889 -1.273 -0.865 1.00 0.00 O HETATM 12 H DAR A 2 0.863 -4.328 0.317 1.00 0.00 H HETATM 13 HA DAR A 2 1.936 -2.225 2.255 1.00 0.00 H HETATM 14 HB2 DAR A 2 -0.394 -2.119 0.285 1.00 0.00 H HETATM 15 HB3 DAR A 2 0.159 -0.764 1.258 1.00 0.00 H HETATM 16 HG2 DAR A 2 -0.301 -2.137 3.365 1.00 0.00 H HETATM 17 HG3 DAR A 2 -1.003 -3.398 2.361 1.00 0.00 H HETATM 18 HD2 DAR A 2 -1.969 -0.468 2.549 1.00 0.00 H HETATM 19 HD3 DAR A 2 -2.717 -1.836 3.368 1.00 0.00 H HETATM 20 HE DAR A 2 -2.956 -2.733 0.769 1.00 0.00 H HETATM 21 HH11 DAR A 2 -5.248 -0.696 -0.735 1.00 0.00 H HETATM 22 HH12 DAR A 2 -4.354 -2.299 -0.707 1.00 0.00 H HETATM 23 HH21 DAR A 2 -4.889 0.780 0.732 1.00 0.00 H HETATM 24 HH22 DAR A 2 -3.671 0.494 2.075 1.00 0.00 H HETATM 25 N DGL A 3 3.759 -1.637 0.359 1.00 0.00 N HETATM 26 CA DGL A 3 4.699 -0.979 -0.604 1.00 0.00 C HETATM 27 C DGL A 3 4.316 0.446 -1.120 1.00 0.00 C HETATM 28 O DGL A 3 4.485 0.727 -2.311 1.00 0.00 O HETATM 29 CB DGL A 3 6.170 -1.082 -0.103 1.00 0.00 C HETATM 30 CG DGL A 3 6.641 -0.196 1.079 1.00 0.00 C HETATM 31 CD DGL A 3 6.009 -0.517 2.437 1.00 0.00 C HETATM 32 OE1 DGL A 3 6.454 -1.479 3.101 1.00 0.00 O HETATM 33 OE2 DGL A 3 5.060 0.191 2.844 1.00 0.00 O HETATM 34 H DGL A 3 4.145 -2.152 1.158 1.00 0.00 H HETATM 35 HA DGL A 3 4.665 -1.622 -1.504 1.00 0.00 H HETATM 36 HB2 DGL A 3 6.830 -0.851 -0.961 1.00 0.00 H HETATM 37 HB3 DGL A 3 6.407 -2.140 0.128 1.00 0.00 H HETATM 38 HG2 DGL A 3 6.481 0.871 0.838 1.00 0.00 H HETATM 39 HG3 DGL A 3 7.738 -0.295 1.179 1.00 0.00 H