10 20 30 40 50 60 70 80 1N37 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 25-OCT-02 1N37
TITLE NMR SOLUTION STRUCTURE OF THE ANTHRACYCLINE RESPINOMYCIN D TITLE 2 INTERCALATION COMPLEX WITH A DOUBLE STRANDED DNA MOLECULE TITLE 3 (AGACGTCT)2
COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*AP*GP*AP*CP*GP*TP*CP*T)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES
KEYWDS DRUG-DNA RECOGNITION, ANTHRACYCLINE ANTIBIOTCS, KEYWDS 2 RESPINOMYCIN D, MOLECULAR DYNAMICS SIMULATIONS, NMR KEYWDS 3 SPECTROSCOPY
EXPDTA SOLUTION NMR
AUTHOR A.J.MAYNARD,H.E.L.WILLIAMS,M.S.SEARLE
REVDAT 2 24-FEB-09 1N37 1 VERSN REVDAT 1 28-JAN-03 1N37 0
JRNL AUTH M.S.SEARLE,A.J.MAYNARD,H.E.L.WILLIAMS JRNL TITL DNA RECOGNITION BY THE ANTHRACYCLINE ANTIBIOTIC JRNL TITL 2 RESPINOMYCIN D: NMR STRUCTURE OF THE INTERCALATION JRNL TITL 3 COMPLEX WITH D(AGACGTCT)2 JRNL REF ORG.BIOMOL.CHEM. V. 1 60 2003 JRNL REFN ISSN 1477-0520 JRNL PMID 12929391 JRNL DOI 10.1039/B208622K
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SANDER(AMBER) 4.1 REMARK 3 AUTHORS : PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM,FERGUSON, REMARK 3 SEIBEL,SINGH,WEINER,KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: SAMPLE WAS SUBJECTED TO 500PS OF REMARK 3 RESTRAINED MOLECULAR DYNAMICS. USING THE AMBER94 FORCE FIELD
REMARK 4 REMARK 4 1N37 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-NOV-02. REMARK 100 THE RCSB ID CODE IS RCSB017461.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 100MM NACL 10MM NA2HPO4 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : RESPINOMYCIN D, D(AGACGTCT)2, REMARK 210 TSP, NAN3, NA-ETDA REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, 2D TOCSY, DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SANDER(AMBER) 4.1 REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 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 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 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DA A 1 C4 - C5 - C6 ANGL. DEV. = -3.7 DEGREES REMARK 500 DA A 1 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DA A 1 N1 - C6 - N6 ANGL. DEV. = -6.1 DEGREES REMARK 500 DA A 3 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DA A 3 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DA A 3 N1 - C6 - N6 ANGL. DEV. = -4.4 DEGREES REMARK 500 DC A 4 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 DG A 5 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DT A 6 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 DT A 6 C6 - C5 - C7 ANGL. DEV. = -5.5 DEGREES REMARK 500 DC A 7 N1 - C2 - O2 ANGL. DEV. = 3.9 DEGREES REMARK 500 DC A 7 N3 - C2 - O2 ANGL. DEV. = -5.7 DEGREES REMARK 500 DT A 8 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DT A 8 C6 - C5 - C7 ANGL. DEV. = -4.5 DEGREES REMARK 500 DA B 9 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 DA B 9 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 DA B 9 N1 - C6 - N6 ANGL. DEV. = -5.5 DEGREES REMARK 500 DG B 10 O4' - C1' - N9 ANGL. DEV. = 5.9 DEGREES REMARK 500 DA B 11 C4 - C5 - C6 ANGL. DEV. = -3.7 DEGREES REMARK 500 DA B 11 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 DA B 11 N1 - C6 - N6 ANGL. DEV. = -6.0 DEGREES REMARK 500 DC B 12 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 DG B 13 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 DT B 14 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 DC B 15 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 DT B 16 O4' - C1' - N1 ANGL. DEV. = 1.9 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 DG B 10 0.07 SIDE_CHAIN REMARK 500 DA B 11 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 RSD B 17
DBREF 1N37 A 1 8 PDB 1N37 1N37 1 8 DBREF 1N37 B 9 16 PDB 1N37 1N37 9 16
SEQRES 1 A 8 DA DG DA DC DG DT DC DT SEQRES 1 B 8 DA DG DA DC DG DT DC DT
HET RSD B 17 146
HETNAM RSD RESPINOMYCIN D
FORMUL 3 RSD C51 H75 N2 O22 1+
SITE 1 AC1 6 DC A 4 DG A 5 DT A 6 DC B 12 SITE 2 AC1 6 DG B 13 DT B 14
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