2GYJ - Header Asymmetric Unit

HEADER 09-MAY-06 2GYJ

TITLE MODEL STRUCTURE OF DNA DODECAMER D(CGCGAATTCGCG)2 BOUND TO TITLE 2 5-(2-IMIDAZOLINYL)-2-[2-(2-IMIDAZOLINYL)-5- TITLE 3 BENZIMIDAZOLYL]BENZIMIDAZOLE

COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)- COMPND 3 3'; COMPND 4 CHAIN: A, B; COMPND 5 ENGINEERED: YES

SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: MODEL BUILT

KEYWDS MODEL BUILT, MINOR GROOVE BINDING, DNA-DRUG, BENZIMIDAZOLE KEYWDS 2 DERIVATIVE

EXPDTA THEORETICAL MODEL

AUTHOR SAHER A SHAIKH

REVDAT 1 17-OCT-06 2GYJ 0

JRNL AUTH SAHER A SHAIKH,B JAYARAM JRNL TITL A SWIFT ALL-ATOM ENERGY BASED COMPUTATIONAL JRNL TITL 2 PROTOCOL TO PREDICT DNA-DRUG BINDING AFFINITY AND JRNL TITL 3 DELTATM JRNL REF TO BE PUBLISHED 2006 JRNL REFN

REMARK 1

REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 8 REMARK 3 AUTHORS : D.A. CASE, T.A. DARDEN, T.E. CHEATHAM, III, REMARK 3 C.L. SIMMERLING, J. WANG, R.E. DUKE, R. LUO, REMARK 3 K.M. MERZ, B. WANG, D.A. PEARLMAN, M. CROWLEY, REMARK 3 S. BROZELL, V. TSUI, H. GOHLKE, J. MONGAN, V. REMARK 3 HORNAK, G. CUI, P. BEROZA, C. SCHAFMEISTER, J.W. REMARK 3 CALDWELL, W.S. ROSS, AND P.A. KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL

REMARK 4 REMARK 4 2GYJ COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998

REMARK 100 REMARK 100 THIS ENTRY WAS DEPOSITED AT RCSB ON 09-MAY-2006. REMARK 100 THE RCSB ID CODE IS RCSB037705.

REMARK 105 REMARK 105 THE PROTEIN DATA BANK HAS ADOPTED THE SACCHARIDE CHEMISTS REMARK 105 NOMENCLATURE FOR ATOMS OF THE DEOXYRIBOSE/RIBOSE MOIETY REMARK 105 RATHER THAN THAT OF THE NUCLEOSIDE CHEMISTS. THE RING REMARK 105 OXYGEN ATOM IS LABELLED O4* INSTEAD OF O1*.

REMARK 220 REMARK 220 EXPERIMENTAL DETAILS REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING REMARK 220 REMARK 220 REMARK: MODEL BUILDING FOLLOWED BY OPTIMIZATION BY ENERGY REMARK 220 MINIMIZATION AND MOLECULAR DYNAMICS SIMULATIONS WITH REMARK 220 EXPLICIT SOLVENT AND COUNTERIONS. THIS THEORETICAL MODEL REMARK 220 ENTRY WAS NOT ANNOTATED AND NOT VALIDATED BY THE WWPDB REMARK 220 STAFF AND THEREFORE MAY NOT CONFORM TO THE PDB FORMAT.

REMARK 225 REMARK 225 THEORETICAL MODEL REMARK 225 THE COORDINATES IN THIS ENTRY REPRESENT A MODEL STRUCTURE. REMARK 225 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT CRYST1 AND REMARK 225 SCALE RECORDS BE INCLUDED, BUT THE VALUES ON THESE REMARK 225 RECORDS ARE MEANINGLESS.

REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2GY6 RELATED DB: PDB REMARK 900 RELATED ID: 2GY8 RELATED DB: PDB REMARK 900 RELATED ID: 2GYE RELATED DB: PDB REMARK 900 RELATED ID: 2GYF RELATED DB: PDB REMARK 900 RELATED ID: 2GYG RELATED DB: PDB REMARK 900 RELATED ID: 2GYH RELATED DB: PDB

SEQRES 1 A 12 C G C G A A T T C G C G SEQRES 1 B 12 C G C G A A T T C G C G

HET 5A7 25 54

FORMUL 3 5A7

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