PDB Short entry for 1AO1 HEADER DNA 16-JUL-97 1AO1 TITLE INTERACTIONS OF DEGLYCOSYLATED COBALT(III)-PEPLEOMYCIN WITH DNA, NMR, TITLE 2 MINIMIZED AVERAGE STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*GP*TP*AP*CP*G)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: DEGLYCOSYLATED PEPLEOMYCIN IS A DNA CLEAVING AGENT COMPND 6 WITH ANTITUMOR ACTIVITY SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS ANTICANCER DRUGS, DEGLYCOSYLATED PEPLEOMYCIN, BLEOMYCINS, DNA, DNA KEYWDS 2 CLEAVAGE, TWO-DIMENSIONAL NMR, SOLUTION STRUCTURES, DEOXYRIBONUCLEIC KEYWDS 3 ACID EXPDTA SOLUTION NMR AUTHOR J.CACERES-CORTES,H.SUGIYAMA,K.IKUDOME,I.SAITO,A.H.-J.WANG REVDAT 4 16-FEB-22 1AO1 1 REMARK REVDAT 3 24-FEB-09 1AO1 1 VERSN REVDAT 2 01-APR-03 1AO1 1 JRNL REVDAT 1 17-SEP-97 1AO1 0 JRNL AUTH J.CACERES-CORTES,H.SUGIYAMA,K.IKUDOME,I.SAITO,A.H.WANG JRNL TITL INTERACTIONS OF DEGLYCOSYLATED COBALT(III)-PEPLEOMYCIN JRNL TITL 2 (GREEN FORM) WITH DNA BASED ON NMR STRUCTURAL STUDIES,. JRNL REF BIOCHEMISTRY V. 36 9995 1997 JRNL REFN ISSN 0006-2960 JRNL PMID 9254594 JRNL DOI 10.1021/BI9708951 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN THE REMARK 3 JRNL CITATION ABOVE. REMARK 4 REMARK 4 1AO1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000171048. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 275 REMARK 210 PH : 6.9 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : UNITY 750; VXR 500 REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR, SPEDREF REMARK 210 METHOD USED : NOE-RMD REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : MINIMIZED AVERAGE REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: NULL 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 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 H1' DG A 6 O4 PL1 B 13 1.49 REMARK 500 HO3' DG A 6 O4 PL1 B 13 1.56 REMARK 500 N3 DG B 8 HF2 PL1 B 13 1.58 REMARK 500 O5' DA B 10 HO2 PL1 B 13 1.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 DT A 3 C5 DT A 3 C7 0.048 REMARK 500 DA B 10 C5' DA B 10 C4' 0.055 REMARK 500 REMARK 500 REMARK: NULL 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 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DT A 3 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 DA A 4 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DG A 6 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DG B 8 C4' - C3' - C2' ANGL. DEV. = -6.4 DEGREES REMARK 500 DG B 8 O4' - C1' - C2' ANGL. DEV. = -10.5 DEGREES REMARK 500 DG B 8 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DG B 8 C8 - N9 - C4 ANGL. DEV. = -3.2 DEGREES REMARK 500 DT B 9 N1 - C1' - C2' ANGL. DEV. = -21.4 DEGREES REMARK 500 DT B 9 O4' - C1' - N1 ANGL. DEV. = 14.9 DEGREES REMARK 500 DT B 9 C3' - O3' - P ANGL. DEV. = -7.8 DEGREES REMARK 500 DA B 10 C5' - C4' - O4' ANGL. DEV. = 7.9 DEGREES REMARK 500 DA B 10 C1' - O4' - C4' ANGL. DEV. = 4.6 DEGREES REMARK 500 DA B 10 O4' - C1' - N9 ANGL. DEV. = -4.4 DEGREES REMARK 500 DA B 10 C3' - O3' - P ANGL. DEV. = 9.1 DEGREES REMARK 500 DC B 11 C1' - O4' - C4' ANGL. DEV. = -6.6 DEGREES REMARK 500 DC B 11 O4' - C1' - N1 ANGL. DEV. = 3.1 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 DC A 1 0.07 SIDE CHAIN REMARK 500 DG A 2 0.09 SIDE CHAIN REMARK 500 DG A 6 0.05 SIDE CHAIN REMARK 500 DT B 9 0.07 SIDE CHAIN REMARK 500 DC B 11 0.07 SIDE CHAIN REMARK 500 DG B 12 0.08 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 PL1 B 13 DBREF 1AO1 A 1 6 PDB 1AO1 1AO1 1 6 DBREF 1AO1 B 7 12 PDB 1AO1 1AO1 7 12 SEQRES 1 A 6 DC DG DT DA DC DG SEQRES 1 B 6 DC DG DT DA DC DG HET PL1 B 13 147 HETNAM PL1 COBALT (III)-DEGLYCOPEPLEOMYCIN FORMUL 3 PL1 C48 H68 CO N17 O12 S2 1+ SITE 1 AC1 8 DT A 3 DA A 4 DC A 5 DG A 6 SITE 2 AC1 8 DG B 8 DT B 9 DA B 10 DC 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