HEADER DNA/ANTIBIOTIC 18-APR-94 173D TITLE MULTIPLE BINDING MODES OF ANTICANCER DRUG ACTINOMYCIN D: X-RAY, TITLE 2 MOLECULAR MODELING, AND SPECTROSCOPIC STUDIES OF D(GAAGCTTC)2- TITLE 3 ACTINOMYCIN D COMPLEXES AND ITS HOST DNA 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, D; 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, ANTIBIOTIC, ANTITUMOR, ANTICANCER, CHROMOPHORE, KEYWDS 2 DEPSIPEPTIDE, DNA-ANTIBIOTIC COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.KAMITORI,F.TAKUSAGAWA REVDAT 11 20-NOV-24 173D 1 REMARK REVDAT 10 10-JUL-24 173D 1 COMPND FORMUL LINK REVDAT 9 15-NOV-23 173D 1 LINK ATOM REVDAT 8 01-NOV-17 173D 1 REMARK REVDAT 7 15-FEB-12 173D 1 REMARK REVDAT 6 27-JUL-11 173D 1 REMARK REVDAT 5 13-JUL-11 173D 1 VERSN REVDAT 4 24-FEB-09 173D 1 VERSN REVDAT 3 19-JUL-02 173D 5 REVDAT 2 27-NOV-00 173D 5 REVDAT 1 15-OCT-94 173D 0 JRNL AUTH S.KAMITORI,F.TAKUSAGAWA JRNL TITL MULTIPLE BINDING MODES OF ANTICANCER DRUG ACTINOMYCIN D: JRNL TITL 2 X-RAY, MOLECULAR MODELING, AND SPECTROSCOPIC STUDIES OF JRNL TITL 3 D(GAAGCTTC)2-ACTINOMYCIN D COMPLEXES AND ITS HOST DNA JRNL REF J.AM.CHEM.SOC. V. 116 4154 1994 JRNL REFN ISSN 0002-7863 JRNL DOI 10.1021/JA00089A002 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) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 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 : 1016 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) : 0.202 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 : 94 REMARK 3 NUCLEIC ACID ATOMS : 322 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 96 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) : 0.037 REMARK 3 BOND ANGLES (DEGREES) : 5.900 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 173D 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_1000170164. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 123.00 REMARK 200 PH : 7.00 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL 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 : RIGAKU AFC-5R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 1016 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 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 (%): 57.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.88 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: F 2 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y+1/2,Z+1/2 REMARK 290 7555 -X,Y+1/2,-Z+1/2 REMARK 290 8555 X,-Y+1/2,-Z+1/2 REMARK 290 9555 X+1/2,Y,Z+1/2 REMARK 290 10555 -X+1/2,-Y,Z+1/2 REMARK 290 11555 -X+1/2,Y,-Z+1/2 REMARK 290 12555 X+1/2,-Y,-Z+1/2 REMARK 290 13555 X+1/2,Y+1/2,Z REMARK 290 14555 -X+1/2,-Y+1/2,Z REMARK 290 15555 -X+1/2,Y+1/2,-Z REMARK 290 16555 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 30.70500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 27.12500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 30.70500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 27.12500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 30.70500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 27.12500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 30.70500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 27.12500 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 34.95000 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 27.12500 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 34.95000 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 27.12500 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 34.95000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 27.12500 REMARK 290 SMTRY1 12 1.000000 0.000000 0.000000 34.95000 REMARK 290 SMTRY2 12 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 27.12500 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 34.95000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 30.70500 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 14 -1.000000 0.000000 0.000000 34.95000 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 30.70500 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 15 -1.000000 0.000000 0.000000 34.95000 REMARK 290 SMTRY2 15 0.000000 1.000000 0.000000 30.70500 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 16 1.000000 0.000000 0.000000 34.95000 REMARK 290 SMTRY2 16 0.000000 -1.000000 0.000000 30.70500 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2990 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 34.95000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 30.70500 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 2810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 O5 PXZ C 6 LIES ON A SPECIAL POSITION. REMARK 375 N10 PXZ C 6 LIES ON A SPECIAL POSITION. REMARK 375 O5 PXZ D 6 LIES ON A SPECIAL POSITION. REMARK 375 N10 PXZ D 6 LIES ON A SPECIAL POSITION. 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, D 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 THR C 7 REMARK 465 DVA C 8 REMARK 465 PRO C 9 REMARK 465 SAR C 10 REMARK 465 MVA C 11 REMARK 465 THR D 1 REMARK 465 DVA D 2 REMARK 465 PRO D 3 REMARK 465 SAR D 4 REMARK 465 MVA D 5 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 C11 PXZ C 6 C11 PXZ C 6 2555 2.16 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 DG A 1 C2' DG A 1 C1' -0.069 REMARK 500 DA A 2 C5' DA A 2 C4' 0.057 REMARK 500 DA A 2 N9 DA A 2 C4 0.042 REMARK 500 DA A 3 C4' DA A 3 C3' -0.062 REMARK 500 DG A 4 C3' DG A 4 C2' -0.093 REMARK 500 DG A 4 O3' DG A 4 C3' 0.126 REMARK 500 DC A 5 P DC A 5 O5' 0.078 REMARK 500 DC A 5 C5' DC A 5 C4' 0.075 REMARK 500 DC A 8 C4' DC A 8 C3' 0.064 REMARK 500 DG B 9 C5' DG B 9 C4' 0.055 REMARK 500 DG B 9 O3' DA B 10 P 0.104 REMARK 500 DA B 10 C6 DA B 10 N1 -0.043 REMARK 500 DA B 11 O4' DA B 11 C1' 0.076 REMARK 500 DG B 12 C4' DG B 12 C3' -0.078 REMARK 500 DG B 12 O3' DG B 12 C3' 0.118 REMARK 500 DG B 12 C2 DG B 12 N3 0.057 REMARK 500 DG B 12 C5 DG B 12 C6 -0.086 REMARK 500 DG B 12 C5 DG B 12 N7 -0.048 REMARK 500 DG B 12 N7 DG B 12 C8 -0.067 REMARK 500 DC B 13 P DC B 13 O5' 0.142 REMARK 500 DC B 13 C2' DC B 13 C1' 0.069 REMARK 500 DT B 14 P DT B 14 O5' 0.117 REMARK 500 DT B 14 C5' DT B 14 C4' 0.045 REMARK 500 DC B 16 P DC B 16 O5' 0.102 REMARK 500 DC B 16 C5' DC B 16 C4' 0.087 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 C5' - C4' - O4' ANGL. DEV. = 8.0 DEGREES REMARK 500 DG A 1 C2' - C3' - O3' ANGL. DEV. = -17.1 DEGREES REMARK 500 DG A 1 C4' - C3' - C2' ANGL. DEV. = -7.6 DEGREES REMARK 500 DG A 1 O4' - C1' - N9 ANGL. DEV. = 7.5 DEGREES REMARK 500 DG A 1 N1 - C6 - O6 ANGL. DEV. = 5.7 DEGREES REMARK 500 DG A 1 C5 - C6 - O6 ANGL. DEV. = -4.8 DEGREES REMARK 500 DG A 1 C3' - O3' - P ANGL. DEV. = 18.6 DEGREES REMARK 500 DA A 2 O3' - P - O5' ANGL. DEV. = -14.2 DEGREES REMARK 500 DA A 2 O4' - C1' - N9 ANGL. DEV. = 9.7 DEGREES REMARK 500 DA A 2 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DA A 3 O4' - C4' - C3' ANGL. DEV. = -13.9 DEGREES REMARK 500 DA A 3 C1' - O4' - C4' ANGL. DEV. = -6.4 DEGREES REMARK 500 DA A 3 N9 - C1' - C2' ANGL. DEV. = 15.9 DEGREES REMARK 500 DA A 3 C6 - N1 - C2 ANGL. DEV. = 3.9 DEGREES REMARK 500 DG A 4 O4' - C4' - C3' ANGL. DEV. = -8.4 DEGREES REMARK 500 DG A 4 C5' - C4' - C3' ANGL. DEV. = -12.4 DEGREES REMARK 500 DG A 4 C5' - C4' - O4' ANGL. DEV. = 8.6 DEGREES REMARK 500 DG A 4 C4' - C3' - O3' ANGL. DEV. = 17.6 DEGREES REMARK 500 DG A 4 C4' - C3' - C2' ANGL. DEV. = 6.0 DEGREES REMARK 500 DG A 4 C3' - C2' - C1' ANGL. DEV. = -7.0 DEGREES REMARK 500 DG A 4 N9 - C1' - C2' ANGL. DEV. = 9.2 DEGREES REMARK 500 DG A 4 O4' - C1' - N9 ANGL. DEV. = 9.4 DEGREES REMARK 500 DG A 4 C3' - O3' - P ANGL. DEV. = 12.5 DEGREES REMARK 500 DC A 5 O4' - C4' - C3' ANGL. DEV. = -5.5 DEGREES REMARK 500 DC A 5 C4' - C3' - C2' ANGL. DEV. = -6.1 DEGREES REMARK 500 DC A 5 O4' - C1' - C2' ANGL. DEV. = -5.4 DEGREES REMARK 500 DC A 5 O4' - C1' - N1 ANGL. DEV. = 11.7 DEGREES REMARK 500 DT A 6 O4' - C4' - C3' ANGL. DEV. = -3.9 DEGREES REMARK 500 DT A 6 C5' - C4' - C3' ANGL. DEV. = 8.3 DEGREES REMARK 500 DT A 6 O4' - C1' - N1 ANGL. DEV. = 11.0 DEGREES REMARK 500 DT A 6 N3 - C2 - O2 ANGL. DEV. = -4.0 DEGREES REMARK 500 DT A 6 C6 - C5 - C7 ANGL. DEV. = -4.5 DEGREES REMARK 500 DT A 7 C4' - C3' - C2' ANGL. DEV. = -4.5 DEGREES REMARK 500 DT A 7 O4' - C1' - C2' ANGL. DEV. = -12.3 DEGREES REMARK 500 DT A 7 O4' - C1' - N1 ANGL. DEV. = 10.9 DEGREES REMARK 500 DT A 7 C2 - N3 - C4 ANGL. DEV. = -4.2 DEGREES REMARK 500 DT A 7 C4 - C5 - C6 ANGL. DEV. = 4.2 DEGREES REMARK 500 DT A 7 C6 - C5 - C7 ANGL. DEV. = -6.6 DEGREES REMARK 500 DC A 8 C5' - C4' - O4' ANGL. DEV. = -12.3 DEGREES REMARK 500 DC A 8 O4' - C1' - N1 ANGL. DEV. = 14.4 DEGREES REMARK 500 DC A 8 C2 - N1 - C1' ANGL. DEV. = -6.7 DEGREES REMARK 500 DG B 9 N9 - C1' - C2' ANGL. DEV. = 9.8 DEGREES REMARK 500 DG B 9 O4' - C1' - N9 ANGL. DEV. = 10.3 DEGREES REMARK 500 DG B 9 C4 - C5 - N7 ANGL. DEV. = -4.1 DEGREES REMARK 500 DG B 9 C8 - N9 - C4 ANGL. DEV. = -4.1 DEGREES REMARK 500 DG B 9 N9 - C4 - C5 ANGL. DEV. = 5.3 DEGREES REMARK 500 DG B 9 N1 - C6 - O6 ANGL. DEV. = -6.9 DEGREES REMARK 500 DG B 9 C5 - C6 - O6 ANGL. DEV. = 6.9 DEGREES REMARK 500 DG B 9 C3' - O3' - P ANGL. DEV. = 7.5 DEGREES REMARK 500 DA B 10 O5' - C5' - C4' ANGL. DEV. = -5.0 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 111 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 DVA D 8 -95.07 -16.04 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 0.06 SIDE CHAIN REMARK 500 DA B 10 0.08 SIDE CHAIN REMARK 500 DT B 15 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 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN D 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: 2D55 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 REMARK 900 RELATED ID: 172D RELATED DB: PDB DBREF 173D A 1 8 PDB 173D 173D 1 8 DBREF 173D B 9 16 PDB 173D 173D 9 16 DBREF 173D C 1 11 NOR NOR00228 NOR00228 1 11 DBREF 173D D 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 SEQRES 1 D 11 THR DVA PRO SAR MVA PXZ THR DVA PRO SAR MVA HET DVA C 2 7 HET SAR C 4 5 HET MVA C 5 8 HET PXZ C 6 13 HET PXZ D 6 13 HET DVA D 8 7 HET SAR D 10 5 HET MVA D 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 2(C16 H12 N2 O6) FORMUL 5 HOH *96(H2 O) LINK C THR C 1 N DVA C 2 1555 1555 1.33 LINK OG1 THR C 1 C MVA C 5 1555 1555 1.40 LINK N THR C 1 C0 PXZ C 6 1555 1555 1.33 LINK C DVA C 2 N PRO C 3 1555 1555 1.34 LINK C PRO C 3 N SAR C 4 1555 1555 1.38 LINK C SAR C 4 N MVA C 5 1555 1555 1.35 LINK N10 PXZ C 6 C11 PXZ C 6 1555 2555 1.31 LINK O5 PXZ C 6 C12 PXZ C 6 1555 2555 1.28 LINK N10 PXZ D 6 C11 PXZ D 6 1555 14555 1.43 LINK O5 PXZ D 6 C12 PXZ D 6 1555 14555 1.44 LINK C0 PXZ D 6 N THR D 7 1555 1555 1.37 LINK C THR D 7 N DVA D 8 1555 1555 1.35 LINK OG1 THR D 7 C MVA D 11 1555 1555 1.39 LINK C DVA D 8 N PRO D 9 1555 1555 1.35 LINK C PRO D 9 N SAR D 10 1555 1555 1.37 LINK C SAR D 10 N MVA D 11 1555 1555 1.37 CISPEP 1 DVA C 2 PRO C 3 0 -4.23 CISPEP 2 PRO C 3 SAR C 4 0 3.45 CISPEP 3 DVA D 8 PRO D 9 0 -16.94 CISPEP 4 PRO D 9 SAR D 10 0 3.51 SITE 1 AC1 7 DG A 4 DC A 5 DT A 6 DA B 11 SITE 2 AC1 7 HOH C2004 HOH C2005 HOH C2006 SITE 1 AC2 7 DG B 12 DC B 13 DT B 14 DT B 15 SITE 2 AC2 7 HOH B2025 HOH D2005 HOH D2009 CRYST1 69.900 61.410 54.250 90.00 90.00 90.00 F 2 2 2 32 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 0.014306 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016284 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018433 0.00000