HEADER DNA 30-JUL-13 4BZT TITLE THE SOLUTION STRUCTURE OF THE MLN 944-D(ATGCAT)2 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA; COMPND 3 CHAIN: A, B; COMPND 4 OTHER_DETAILS: THE DNA CONFORMATION IS IN THE FORM OF B-DNA. SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 OTHER_DETAILS: EUROGENTEC KEYWDS BIS(PHENAZINE-1-CARBOXAMIDES), DNA, INTERCALATION, DRUG DESIGN, KEYWDS 2 ANTICANCER DRUG. EXPDTA SOLUTION NMR MDLTYP MINIMIZED AVERAGE AUTHOR A.SEROBIAN,D.S.THOMAS,G.E.BALL,W.A.DENNY,L.P.G.WAKELIN REVDAT 3 03-SEP-14 4BZT 1 JRNL REVDAT 2 04-SEP-13 4BZT 1 COMPND REVDAT 1 21-AUG-13 4BZT 0 JRNL AUTH A.SEROBIAN,D.S.THOMAS,G.E.BALL,W.A.DENNY,L.P.G.WAKELIN JRNL TITL THE SOLUTION STRUCTURE OF BIS(PHENAZINE-1-CARBOXAMIDE)-DNA JRNL TITL 2 COMPLEXES: MLN 944 BINDING CORRECTED AND EXTENDED. JRNL REF BIOPOLYMERS V. 101 1099 2014 JRNL REFN ISSN 0006-3525 JRNL PMID 24898663 JRNL DOI 10.1002/BIP.22513 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : D.A.CASE,ET.AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4BZT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-AUG-13. REMARK 100 THE PDBE ID CODE IS EBI-57846. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 288.0 REMARK 210 PH : 5.0 REMARK 210 IONIC STRENGTH : 80MM REMARK 210 PRESSURE : 1.0 ATM REMARK 210 SAMPLE CONTENTS : 10% WATER/90% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY, COSY, TOCSY, 31P REMARK 210 HSQC, 15N HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 3.1 REMARK 210 METHOD USED : AMBER REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : DISTANCE RESTRAINTS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: NONE 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 DA A 1 C4 - C5 - C6 ANGL. DEV. = -3.7 DEGREES REMARK 500 DA A 1 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 DA A 1 N1 - C6 - N6 ANGL. DEV. = -5.2 DEGREES REMARK 500 DA A 1 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG A 3 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DC A 4 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DA A 5 C4 - C5 - C6 ANGL. DEV. = -3.6 DEGREES REMARK 500 DA A 5 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DA A 5 N1 - C6 - N6 ANGL. DEV. = -5.4 DEGREES REMARK 500 DA A 5 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DT A 6 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 DA B 7 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 DA B 7 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 DA B 7 N1 - C6 - N6 ANGL. DEV. = -5.5 DEGREES REMARK 500 DA B 7 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT B 8 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DG B 9 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DC B 10 N3 - C2 - O2 ANGL. DEV. = -4.4 DEGREES REMARK 500 DC B 10 N3 - C4 - C5 ANGL. DEV. = 2.5 DEGREES REMARK 500 DA B 11 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DA B 11 N1 - C6 - N6 ANGL. DEV. = -4.4 DEGREES REMARK 500 DA B 11 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DT B 12 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 DT B 12 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DA A 5 0.07 SIDE CHAIN REMARK 500 DT B 8 0.07 SIDE CHAIN 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 XR2 A 13 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4BZU RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE MLN 944-D(TATGCATA)2 REMARK 900 COMPLEX REMARK 900 RELATED ID: 4BZV RELATED DB: PDB REMARK 900 THE SOLUTION STRUCTURE OF THE MLN 944-D(TACGCGTA)2 REMARK 900 COMPLEX DBREF 4BZT A 1 6 PDB 4BZT 4BZT 1 6 DBREF 4BZT B 7 12 PDB 4BZT 4BZT 7 12 SEQRES 1 A 6 DA DT DG DC DA DT SEQRES 1 B 6 DA DT DG DC DA DT HET XR2 A 13 80 HETNAM XR2 1-METHYL-9-[12-(9-METHYLPHENAZIN-10-IUM-1-YL) HETNAM 2 XR2 -12-OXO-2,11-DIAZA-5,8-DIAZONIADODEC-1-ANOYL] HETNAM 3 XR2 PHENAZIN-10-IUM FORMUL 2 XR2 C34 H38 N8 O2 4+ SITE 1 AC1 8 DT A 2 DG A 3 DC A 4 DA A 5 SITE 2 AC1 8 DT B 8 DG B 9 DC B 10 DA B 11 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 MASTER 138 0 1 0 0 0 2 6 0 0 0 2 END