HEADER DNA/ANTIBIOTIC 01-MAY-95 2D55 TITLE STRUCTURAL, PHYSICAL AND BIOLOGICAL CHARACTERISTICS OF RNA.DNA BINDING TITLE 2 AGENT N8-ACTINOMYCIN D 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 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 X-RAY DIFFRACTION AUTHOR M.SHINOMIYA,W.CHU,R.G.CARLSON,R.F.WEAVER,F.TAKUSAGAWA REVDAT 6 15-NOV-23 2D55 1 LINK ATOM REVDAT 5 27-JUL-11 2D55 1 ATOM REMARK REVDAT 4 13-JUL-11 2D55 1 VERSN REVDAT 3 24-FEB-09 2D55 1 VERSN REVDAT 2 01-APR-03 2D55 1 JRNL REVDAT 1 15-OCT-95 2D55 0 SPRSDE 15-OCT-95 2D55 1D55 JRNL AUTH S.KAMITORI,F.TAKUSAGAWA JRNL TITL CRYSTAL STRUCTURE OF THE 2:1 COMPLEX BETWEEN D(GAAGCTTC) AND JRNL TITL 2 THE ANTICANCER DRUG ACTINOMYCIN D. JRNL REF J.MOL.BIOL. V. 225 445 1992 JRNL REFN ISSN 0022-2836 JRNL PMID 1593629 JRNL DOI 10.1016/0022-2836(92)90931-9 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.SHINOMIYA,W.CHU,R.G.CARLSON,R.F.WEAVER,F.TAKUSAGAWA REMARK 1 TITL STRUCTURAL, PHYSICAL, AND BIOLOGICAL CHARACTERISTICS OF REMARK 1 TITL 2 RNA.DNA BINDING AGENT N8- ACTINOMYCIN D. REMARK 1 REF BIOCHEMISTRY V. 34 8481 1995 REMARK 1 REFN ISSN 0006-2960 REMARK 1 PMID 7541244 REMARK 1 DOI 10.1021/BI00026A032 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 7.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 1360 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 90 REMARK 3 NUCLEIC ACID ATOMS : 321 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 104 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.019 REMARK 3 BOND ANGLES (DEGREES) : 4.800 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2D55 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY NDB. REMARK 100 THE DEPOSITION ID IS D_1000177978. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 7.00 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : DIFFRACTOMETER REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.00, VAPOR DIFFUSION, TEMPERATURE REMARK 280 277.00K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 25.68500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.04500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 25.68500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 31.04500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 DG B 9 O5' REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 O HOH A 2040 H2 HOH A 2041 1.57 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 DA A 2 P DA A 2 O5' 0.066 REMARK 500 DA A 3 C5' DA A 3 C4' 0.064 REMARK 500 DG A 4 C5' DG A 4 C4' 0.051 REMARK 500 DG A 4 C6 DG A 4 N1 -0.042 REMARK 500 DT A 6 P DT A 6 O5' 0.064 REMARK 500 DT A 6 C5' DT A 6 C4' 0.052 REMARK 500 DT A 7 C5' DT A 7 C4' 0.060 REMARK 500 DT A 7 C5 DT A 7 C7 0.038 REMARK 500 DA B 11 P DA B 11 O5' 0.076 REMARK 500 DA B 11 C5' DA B 11 C4' 0.045 REMARK 500 DG B 12 P DG B 12 O5' 0.076 REMARK 500 DG B 12 C5' DG B 12 C4' 0.049 REMARK 500 DC B 13 O3' DT B 14 P 0.078 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 C1' - O4' - C4' ANGL. DEV. = -8.7 DEGREES REMARK 500 DG A 1 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DG A 1 C3' - O3' - P ANGL. DEV. = 10.2 DEGREES REMARK 500 DA A 2 C1' - O4' - C4' ANGL. DEV. = -11.2 DEGREES REMARK 500 DA A 2 C4' - C3' - C2' ANGL. DEV. = -5.4 DEGREES REMARK 500 DA A 2 O4' - C1' - C2' ANGL. DEV. = -7.6 DEGREES REMARK 500 DA A 2 N9 - C1' - C2' ANGL. DEV. = 18.5 DEGREES REMARK 500 DA A 2 C3' - O3' - P ANGL. DEV. = 7.9 DEGREES REMARK 500 DA A 3 C5' - C4' - O4' ANGL. DEV. = 7.8 DEGREES REMARK 500 DA A 3 C3' - O3' - P ANGL. DEV. = 9.2 DEGREES REMARK 500 DG A 4 P - O5' - C5' ANGL. DEV. = 14.8 DEGREES REMARK 500 DG A 4 C4' - C3' - C2' ANGL. DEV. = -5.1 DEGREES REMARK 500 DG A 4 O4' - C1' - C2' ANGL. DEV. = -5.9 DEGREES REMARK 500 DG A 4 O4' - C1' - N9 ANGL. DEV. = 5.9 DEGREES REMARK 500 DC A 5 C4' - C3' - C2' ANGL. DEV. = -5.1 DEGREES REMARK 500 DT A 6 P - O5' - C5' ANGL. DEV. = 13.1 DEGREES REMARK 500 DT A 6 O4' - C1' - C2' ANGL. DEV. = -5.8 DEGREES REMARK 500 DT A 6 O4' - C1' - N1 ANGL. DEV. = 9.5 DEGREES REMARK 500 DT A 6 C6 - N1 - C2 ANGL. DEV. = -3.2 DEGREES REMARK 500 DT A 6 N3 - C4 - C5 ANGL. DEV. = -3.8 DEGREES REMARK 500 DT A 6 C4 - C5 - C6 ANGL. DEV. = 4.1 DEGREES REMARK 500 DT A 6 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 DT A 6 C6 - C5 - C7 ANGL. DEV. = -4.8 DEGREES REMARK 500 DT A 6 C3' - O3' - P ANGL. DEV. = 11.2 DEGREES REMARK 500 DT A 7 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 DT A 7 C3' - O3' - P ANGL. DEV. = 12.7 DEGREES REMARK 500 DC A 8 C4' - C3' - C2' ANGL. DEV. = -6.7 DEGREES REMARK 500 DC A 8 O4' - C1' - N1 ANGL. DEV. = 7.7 DEGREES REMARK 500 DC A 8 N1 - C2 - O2 ANGL. DEV. = 4.5 DEGREES REMARK 500 DG B 9 O4' - C4' - C3' ANGL. DEV. = -3.9 DEGREES REMARK 500 DG B 9 C1' - O4' - C4' ANGL. DEV. = -11.3 DEGREES REMARK 500 DG B 9 O4' - C1' - N9 ANGL. DEV. = 6.5 DEGREES REMARK 500 DA B 10 O3' - P - O5' ANGL. DEV. = 12.4 DEGREES REMARK 500 DA B 10 N1 - C6 - N6 ANGL. DEV. = 5.7 DEGREES REMARK 500 DA B 10 C5 - C6 - N6 ANGL. DEV. = -6.9 DEGREES REMARK 500 DA B 10 C3' - O3' - P ANGL. DEV. = 8.5 DEGREES REMARK 500 DA B 11 P - O5' - C5' ANGL. DEV. = 15.9 DEGREES REMARK 500 DA B 11 C4' - C3' - O3' ANGL. DEV. = 12.3 DEGREES REMARK 500 DA B 11 O4' - C1' - N9 ANGL. DEV. = 11.6 DEGREES REMARK 500 DA B 11 C3' - O3' - P ANGL. DEV. = 11.1 DEGREES REMARK 500 DG B 12 P - O5' - C5' ANGL. DEV. = 11.6 DEGREES REMARK 500 DG B 12 O4' - C1' - N9 ANGL. DEV. = 7.3 DEGREES REMARK 500 DC B 13 C4' - C3' - O3' ANGL. DEV. = 12.8 DEGREES REMARK 500 DC B 13 O4' - C1' - C2' ANGL. DEV. = -8.6 DEGREES REMARK 500 DC B 13 O4' - C1' - N1 ANGL. DEV. = 9.4 DEGREES REMARK 500 DC B 13 N1 - C2 - O2 ANGL. DEV. = 5.3 DEGREES REMARK 500 DC B 13 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 DC B 13 C3' - O3' - P ANGL. DEV. = 17.1 DEGREES REMARK 500 DT B 14 C5' - C4' - O4' ANGL. DEV. = 6.8 DEGREES REMARK 500 DT B 14 N1 - C1' - C2' ANGL. DEV. = 10.6 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 53 ANGLE DEVIATIONS. 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 A 1 0.09 SIDE CHAIN REMARK 500 DA A 2 0.10 SIDE CHAIN REMARK 500 DA A 3 0.10 SIDE CHAIN REMARK 500 DG A 4 0.08 SIDE CHAIN REMARK 500 DT A 7 0.16 SIDE CHAIN REMARK 500 DC A 8 0.07 SIDE CHAIN REMARK 500 DG B 9 0.07 SIDE CHAIN REMARK 500 DA B 10 0.08 SIDE CHAIN REMARK 500 DG B 12 0.08 SIDE CHAIN REMARK 500 DT B 14 0.17 SIDE CHAIN REMARK 500 DC B 16 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 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: 1DSC RELATED DB: PDB REMARK 900 SOLUTION 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 2D55 A 1 8 PDB 2D55 2D55 1 8 DBREF 2D55 B 9 16 PDB 2D55 2D55 9 16 DBREF 2D55 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 8 HET SAR C 4 5 HET MVA C 5 8 HET PXZ C 6 24 HET DVA C 8 8 HET SAR C 10 5 HET MVA C 11 8 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 FORMUL 4 HOH *104(H2 O) LINK C THR C 1 N DVA C 2 1555 1555 1.35 LINK OG1 THR C 1 C MVA C 5 1555 1555 1.39 LINK N THR C 1 C0 PXZ C 6 1555 1555 1.34 LINK C DVA C 2 N PRO C 3 1555 1555 1.34 LINK C PRO C 3 N SAR C 4 1555 1555 1.34 LINK C SAR C 4 N MVA C 5 1555 1555 1.35 LINK C0' PXZ C 6 N THR C 7 1555 1555 1.34 LINK C THR C 7 N DVA C 8 1555 1555 1.34 LINK OG1 THR C 7 C MVA C 11 1555 1555 1.40 LINK C DVA C 8 N PRO C 9 1555 1555 1.35 LINK C PRO C 9 N SAR C 10 1555 1555 1.37 LINK C SAR C 10 N MVA C 11 1555 1555 1.37 CISPEP 1 DVA C 2 PRO C 3 0 29.13 CISPEP 2 PRO C 3 SAR C 4 0 -1.57 CISPEP 3 DVA C 8 PRO C 9 0 19.32 CISPEP 4 PRO C 9 SAR C 10 0 -18.31 SITE 1 AC1 11 DG A 4 DC A 5 DT A 6 DT A 7 SITE 2 AC1 11 HOH A2009 DA B 11 DG B 12 DC B 13 SITE 3 AC1 11 DT B 14 DT B 15 HOH C2001 CRYST1 51.370 62.090 25.040 90.00 113.80 90.00 C 1 2 1 8 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 0.019467 0.000000 0.008586 0.00000 SCALE2 0.000000 0.016106 0.000000 0.00000 SCALE3 0.000000 0.000000 0.043648 0.00000