PDB Short entry for 1DSC HEADER DNA/ANTIBIOTIC 10-AUG-96 1DSC TITLE NMR STUDY OF DNA (5'-D(*GP*AP*AP*GP*CP*TP*TP*C)-3') SELF-COMPLEMENTARY TITLE 2 DUPLEX COMPLEXED WITH ACTINOMYCIN D, MINIMIZED AVERAGE STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*GP*AP*AP*GP*CP*TP*TP*C)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: ACTINOMYCIN D; COMPND 7 CHAIN: C; COMPND 8 SYNONYM: DACTINOMYCIN SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 ORGANISM_SCIENTIFIC: STREPTOMYCES ANTIBIOTICUS; SOURCE 5 ORGANISM_TAXID: 1890 KEYWDS ACTINOMYCIN D, DACTINOMYCIN, ANTIBIOTIC, ANTI CANCER, ANTITUMOR, KEYWDS 2 CHROMOPHORE, DEPSIPEPTIDE, DNA-ANTIBIOTIC COMPLEX EXPDTA SOLUTION NMR AUTHOR C.LIAN,H.ROBINSON,A.H.-J.WANG REVDAT 5 15-NOV-23 1DSC 1 LINK ATOM REVDAT 4 27-JUL-11 1DSC 1 ATOM REMARK REVDAT 3 13-JUL-11 1DSC 1 VERSN REVDAT 2 24-FEB-09 1DSC 1 VERSN REVDAT 1 07-DEC-96 1DSC 0 JRNL AUTH C.LIAN,H.ROBINSON,A.H.-J.WANG JRNL TITL STRUCTURE OF ACTINOMYCIN D BOUND WITH (GAAGCTTC)2 AND JRNL TITL 2 (GATGCTTC)2 AND ITS BINDING TO THE (CAG)N:(CTG)N TRIPLET JRNL TITL 3 SEQUENCE BY NMR ANALYSIS JRNL REF J.AM.CHEM.SOC. V. 118 8791 1996 JRNL REFN ISSN 0002-7863 JRNL DOI 10.1021/JA961631P REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1DSC 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_1000172919. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 275 REMARK 210 PH : 7.0 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 : 500 MHZ REMARK 210 SPECTROMETER MODEL : 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 : NULL 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 400 REMARK 400 COMPOUND REMARK 400 ACTINOMYCIN D IS A BICYCLIC PEPTIDE, A MEMBER OF THE REMARK 400 ACTINOMYCIN FAMILY. REMARK 400 HERE, ACTINOMYCIN D IS REPRESENTED BY THE SEQUENCE (SEQRES) REMARK 400 REMARK 400 THE ACTINOMYCIN D IS POLYPEPTIDE, A MEMBER OF ANTIBIOTIC CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: ACTINOMYCIN D REMARK 400 CHAIN: C REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: ACTINOMYCIN D CONSISTS OF TWO PENTAMER RINGS LINKED REMARK 400 BY THE CHROMOPHORE (PXZ) 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 DG A 1 C5' DG A 1 C4' 0.046 REMARK 500 DT A 6 C5 DT A 6 C7 0.039 REMARK 500 DG B 9 C5' DG B 9 C4' 0.048 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 1 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DA A 2 O4' - C1' - N9 ANGL. DEV. = 8.6 DEGREES REMARK 500 DA A 3 O4' - C1' - C2' ANGL. DEV. = -5.2 DEGREES REMARK 500 DA A 3 C3' - O3' - P ANGL. DEV. = 9.6 DEGREES REMARK 500 DG A 4 C5' - C4' - O4' ANGL. DEV. = 7.0 DEGREES REMARK 500 DG A 4 O4' - C1' - C2' ANGL. DEV. = -6.6 DEGREES REMARK 500 DC A 5 O4' - C1' - N1 ANGL. DEV. = 8.4 DEGREES REMARK 500 DT A 6 O4' - C4' - C3' ANGL. DEV. = -3.2 DEGREES REMARK 500 DT A 6 C5' - C4' - O4' ANGL. DEV. = 9.2 DEGREES REMARK 500 DT A 6 O4' - C1' - C2' ANGL. DEV. = -8.2 DEGREES REMARK 500 DT A 6 O4' - C1' - N1 ANGL. DEV. = 8.7 DEGREES REMARK 500 DG B 9 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DA B 10 O4' - C1' - N9 ANGL. DEV. = 8.7 DEGREES REMARK 500 DA B 11 O4' - C1' - C2' ANGL. DEV. = -4.8 DEGREES REMARK 500 DA B 11 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 DA B 11 C3' - O3' - P ANGL. DEV. = 12.3 DEGREES REMARK 500 DG B 12 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES REMARK 500 DC B 13 O4' - C1' - N1 ANGL. DEV. = 6.1 DEGREES REMARK 500 DT B 14 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 DT B 14 C6 - C5 - C7 ANGL. DEV. = -4.3 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 8 0.08 SIDE CHAIN REMARK 500 DC B 16 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 CHAIN C OF ACTINOMYCIN D REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1A7Z RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ACTINOMYCIN Z3 REMARK 900 RELATED ID: 209D RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF N8-ACTINOMYCIN D COMPLEXED WITH D(GAAGCTTC)2 REMARK 900 RELATED ID: 1UNM RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF 7-AMINOACTINOMYCIN D COMPLEXED WITH NON- REMARK 900 COMPLEMENTARY DNA REMARK 900 RELATED ID: 1I3W RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ACTINOMYCIN D COMPLEXED WITH DNA (CGATCGATCG)2 REMARK 900 RELATED ID: 1A7Y RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ACTINOMYCIN D REMARK 900 RELATED ID: 1FJA RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF ACTINOMYCIN D COMPLEXED WITH DNA (AAGCGCTT)2 REMARK 900 RELATED ID: 173D RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ACTINOMYCIN D COMPLEXED WITH DNA (GAAGCTTC)2 REMARK 900 RELATED ID: 2D55 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ACTINOMYCIN D COMPLEXED WITH DNA (GAAGCTTC)2 REMARK 900 RELATED ID: 1L1V RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF ACTNIOMYCIN D COMPLEXED WITH MISMATCHED DNA REMARK 900 (GTCACCGAC) REMARK 900 RELATED ID: 316D RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF F8-ACTINOMYCIN D COMPLEXED WITH DNA (GAAGCTTC)2 REMARK 900 RELATED ID: 1DSD RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF ACTINOMYCIN D COMPLEXED WITH DNA (GATGCTTC)2 REMARK 900 RELATED ID: 1MNV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ACTINOMYCIN D COMPLEXED WITH DNA (ATGCTGCAT)2 REMARK 900 RELATED ID: 1UNJ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF 7-AMINO-ACTINOMYCIN D COMPLEXED WITH A NON- REMARK 900 COMPLEMENTARY DNA (TTAGT)2 REMARK 900 RELATED ID: 1OVF RELATED DB: PDB REMARK 900 SOLUTIOM STRUCTURE OF ACTINOMYCIN D COMPLEXED WITH DNA (CCGTTTTGTGG) REMARK 900 2 REMARK 900 RELATED ID: 1QFI RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ACTINOMYCIN X2 DBREF 1DSC A 1 8 PDB 1DSC 1DSC 1 8 DBREF 1DSC B 9 16 PDB 1DSC 1DSC 9 16 DBREF 1DSC C 1 11 NOR NOR00228 NOR00228 1 11 SEQRES 1 A 8 DG DA DA DG DC DT DT DC SEQRES 1 B 8 DG DA DA DG DC DT DT DC SEQRES 1 C 11 THR DVA PRO SAR MVA PXZ THR DVA PRO SAR MVA HET DVA C 2 16 HET SAR C 4 10 HET MVA C 5 19 HET PXZ C 6 32 HET DVA C 8 16 HET SAR C 10 10 HET MVA C 11 19 HETNAM DVA D-VALINE HETNAM SAR SARCOSINE HETNAM MVA N-METHYLVALINE HETNAM PXZ 2-AMINO-1,9-DICARBONYL-4,6-DIMETHYL-10-DEHYDRO- HETNAM 2 PXZ PHENOXAZIN-3-ONE HETSYN PXZ PHENOXAZINE FORMUL 3 DVA 2(C5 H11 N O2) FORMUL 3 SAR 2(C3 H7 N O2) FORMUL 3 MVA 2(C6 H13 N O2) FORMUL 3 PXZ C16 H12 N2 O4 LINK C THR C 1 N DVA C 2 1555 1555 1.30 LINK OG1 THR C 1 C MVA C 5 1555 1555 1.33 LINK N THR C 1 C0 PXZ C 6 1555 1555 1.31 LINK C DVA C 2 N PRO C 3 1555 1555 1.31 LINK C PRO C 3 N SAR C 4 1555 1555 1.30 LINK C SAR C 4 N MVA C 5 1555 1555 1.32 LINK C0' PXZ C 6 N THR C 7 1555 1555 1.30 LINK C THR C 7 N DVA C 8 1555 1555 1.30 LINK OG1 THR C 7 C MVA C 11 1555 1555 1.31 LINK C DVA C 8 N PRO C 9 1555 1555 1.30 LINK C PRO C 9 N SAR C 10 1555 1555 1.31 LINK C SAR C 10 N MVA C 11 1555 1555 1.32 CISPEP 1 DVA C 2 PRO C 3 0 28.91 CISPEP 2 PRO C 3 SAR C 4 0 -0.76 CISPEP 3 DVA C 8 PRO C 9 0 19.63 CISPEP 4 PRO C 9 SAR C 10 0 0.46 SITE 1 AC1 9 DA A 3 DG A 4 DC A 5 DT A 6 SITE 2 AC1 9 DT A 7 DA B 11 DG B 12 DC B 13 SITE 3 AC1 9 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