HEADER DNA/ANTIBIOTIC 28-OCT-04 1XVK TITLE X-RAY STRUCTURE OF AN ECHINOMYCIN-(GCGTACGC)2 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*CP*GP*TP*AP*CP*GP*C)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: ECHINOMYCIN; COMPND 7 CHAIN: B; COMPND 8 SYNONYM: QUINOMYCIN A SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 ORGANISM_SCIENTIFIC: STREPTOMYCES ECHINATUS; SOURCE 5 ORGANISM_TAXID: 67293 KEYWDS BISINTERCALATOR, HOOGSTEEN BASEPAIR, DEPSIPEPTIDE, QUINOXALINE, KEYWDS 2 THIOACETAL, ANTIBIOTIC, ANTITUMOR, DNA-ANTIBIOTIC COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.A.CUESTA-SEIJO,G.M.SHELDRICK REVDAT 5 09-SEP-20 1XVK 1 TITLE REMARK SEQADV LINK REVDAT 4 27-JUL-11 1XVK 1 REMARK REVDAT 3 13-JUL-11 1XVK 1 VERSN REVDAT 2 24-FEB-09 1XVK 1 VERSN REVDAT 1 12-APR-05 1XVK 0 JRNL AUTH J.A.CUESTA-SEIJO,G.M.SHELDRICK JRNL TITL STRUCTURES OF COMPLEXES BETWEEN ECHINOMYCIN AND DUPLEX DNA. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 61 442 2005 JRNL REFN ISSN 0907-4449 JRNL PMID 15805599 JRNL DOI 10.1107/S090744490500137X REMARK 2 REMARK 2 RESOLUTION. 1.26 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.26 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.183 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.183 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1025 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 10337 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 67 REMARK 3 NUCLEIC ACID ATOMS : 161 REMARK 3 HETEROGEN ATOMS : 25 REMARK 3 SOLVENT ATOMS : 56 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 9 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 ANGLE DISTANCES (A) : NULL REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE SKELETON OF ECHINOMYCIN IS NEARLY REMARK 3 SYMMETRIC (NOT MODELLED TO DO SO), THE BRIDGE IS NOT. BOTH REMARK 3 POSSIBLE ORIENTATIONS OF BINDING WERE OBSERVED AND ARE MODELLED REMARK 3 AS DISORDERED/MICROHETE. REMARK 4 REMARK 4 1XVK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-OCT-04. REMARK 100 THE DEPOSITION ID IS D_1000030813. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-DEC-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : SI-111 CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10337 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.260 REMARK 200 RESOLUTION RANGE LOW (A) : 26.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 15.87 REMARK 200 R MERGE (I) : 0.04950 REMARK 200 R SYM (I) : 0.04950 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 28.2500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.26 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 9.78 REMARK 200 R MERGE FOR SHELL (I) : 0.35000 REMARK 200 R SYM FOR SHELL (I) : 0.35000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 6.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MR REMARK 200 SOFTWARE USED: EPMR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG550MME, MGCL2, NAAC, SPERMINE- HCL, REMARK 280 PH 4.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z REMARK 290 10555 -Y,-X,-Z+1/2 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/2 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 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 39.94500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 39.94500 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 39.94500 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 39.94500 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 39.94500 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 39.94500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.3 KCAL/MOL 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 0.500000 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 MG MG A 25 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2004 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2010 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2011 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2012 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2046 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 THE ECHINOMYCIN IS A BICYCLIC OCTADEPSIPEPTIDE, A MEMBER REMARK 400 OF THE QUINOXALINE CLASS OF ANTIBIOTICS. REMARK 400 HERE, ECHINOMYCIN IS REPRESENTED BY GROUPING TOGETHER THE REMARK 400 SEQUENCE (SEQRES) AND TWO LIGANDS (HET) QUI. REMARK 400 REMARK 400 THE ECHINOMYCIN IS CYCLIC DEPSIPEPTIDE, A MEMBER OF ANTIBIOTIC REMARK 400 CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: ECHINOMYCIN REMARK 400 CHAIN: B REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 COMPONENT_2: RESIDUE QUI, 2 COPIES REMARK 400 DESCRIPTION: ECHINOMYCIN IS A BICYCLIC OCTADEPSIPEPTIDE. REMARK 400 BICYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE REMARK 400 C- TERMINI, AND A THIOACETAL BOND BETWEEN RESIDUES 3 REMARK 400 AND 7. THE TWO QUINOXALINE CHROMOPHORES ARE LINKED REMARK 400 TO THE D-SERINE RESIDUES, RESIDUES 1 AND 5. 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 O4' DG A 1 C1' 0.066 REMARK 500 DG A 1 O4' DG A 1 C1' 0.067 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 C4' - C3' - C2' ANGL. DEV. = 6.2 DEGREES REMARK 500 DG A 1 C3' - C2' - C1' ANGL. DEV. = 8.0 DEGREES REMARK 500 DG A 1 N9 - C1' - C2' ANGL. DEV. = 8.7 DEGREES REMARK 500 DG A 1 O4' - C1' - N9 ANGL. DEV. = -8.0 DEGREES REMARK 500 DG A 1 O4' - C1' - N9 ANGL. DEV. = -7.7 DEGREES REMARK 500 DC A 2 O5' - C5' - C4' ANGL. DEV. = -4.8 DEGREES REMARK 500 DC A 2 O4' - C1' - N1 ANGL. DEV. = -8.4 DEGREES REMARK 500 DG A 3 O4' - C1' - N9 ANGL. DEV. = 6.3 DEGREES REMARK 500 DG A 3 C4 - C5 - N7 ANGL. DEV. = 3.0 DEGREES REMARK 500 DG A 3 C8 - N9 - C4 ANGL. DEV. = 2.5 DEGREES REMARK 500 DG A 3 N9 - C4 - C5 ANGL. DEV. = -3.1 DEGREES REMARK 500 DG A 3 N1 - C6 - O6 ANGL. DEV. = 4.6 DEGREES REMARK 500 DG A 3 C5 - C6 - O6 ANGL. DEV. = -4.7 DEGREES REMARK 500 DT A 4 P - O5' - C5' ANGL. DEV. = 11.5 DEGREES REMARK 500 DT A 4 N1 - C1' - C2' ANGL. DEV. = 10.9 DEGREES REMARK 500 DT A 4 O4' - C1' - N1 ANGL. DEV. = -6.9 DEGREES REMARK 500 DT A 4 O4' - C1' - N1 ANGL. DEV. = -8.7 DEGREES REMARK 500 DA A 5 C2 - N3 - C4 ANGL. DEV. = 3.5 DEGREES REMARK 500 DG A 7 O4' - C1' - N9 ANGL. DEV. = 6.4 DEGREES REMARK 500 DC A 8 O4' - C1' - N1 ANGL. DEV. = -5.6 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 25 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A2018 O REMARK 620 2 HOH A2018 O 88.9 REMARK 620 3 HOH A2018 O 88.9 88.9 REMARK 620 4 HOH A2020 O 93.6 176.8 89.2 REMARK 620 5 HOH A2020 O 89.2 93.6 176.8 88.3 REMARK 620 6 HOH A2020 O 176.8 89.2 93.6 88.3 88.3 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 25 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN B OF ECHINOMYCIN REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 185D RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF D(GACGTC) COMPLEXED WITH TRIOSTIN A REMARK 900 RELATED ID: 193D RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF D(ACACGTGT) COMPLEXED WITH QUINOMYCIN UK-6305 REMARK 900 RELATED ID: 1PFE RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF D(GCGTACG) COMPLEXED WITH ECHINOMYCIN - SPACE REMARK 900 GROUP P6322 REMARK 900 RELATED ID: 1VS2 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF D(GCGTACGC) COMPLEXED WITH TRIOSIN A REMARK 900 RELATED ID: 1XVN RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF D(ACGTACGT) COMPLEXED WITH ECHINOMYCIN - SPACE REMARK 900 GROUP P632 REMARK 900 RELATED ID: 1XVR RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF D(CGTACG) COMPLEXED WITH ECHINOMYCIN - SPACE REMARK 900 GROUP C21 REMARK 900 RELATED ID: 2ADW RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF D(ACGTACGT) COMPLEXED WITH ECHINOMYCIN - SPACE REMARK 900 GROUP P42212 REMARK 900 RELATED ID: 2DA8 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF D(GATATC) COMPLEXED WITH A MODIFIED TRIOSTIN REMARK 900 A AT POSITIONS 4 AND 8 REMARK 900 RELATED ID: 3GO3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF D(ACGTACGT) COMPLEXED WITH ECHINOMYCIN - SPACE REMARK 900 GROUP P41212 DBREF 1XVK A 1 8 PDB 1XVK 1XVK 1 8 DBREF 1XVK B 1 8 NOR NOR01126 NOR01126 1 8 SEQADV 1XVK N2C B 3 NOR NOR01126 NCY 3 MICROHETEROGENEITY SEQADV 1XVK NCY B 7 NOR NOR01126 N2C 7 MICROHETEROGENEITY SEQRES 1 A 8 DG DC DG DT DA DC DG DC SEQRES 1 B 8 DSN ALA N2C MVA DSN ALA NCY MVA HET DSN B 1 6 HET N2C B 3 8 HET NCY B 3 7 HET MVA B 4 16 HET DSN B 5 8 HET NCY B 7 7 HET N2C B 7 7 HET MVA B 8 8 HET MG A 25 1 HET QUI B 0 12 HET QUI B 9 12 HETNAM DSN D-SERINE HETNAM N2C N,S-DIMETHYLCYSTEINE HETNAM NCY N-METHYLCYSTEINE HETNAM MVA N-METHYLVALINE HETNAM MG MAGNESIUM ION HETNAM QUI 2-CARBOXYQUINOXALINE FORMUL 2 DSN 2(C3 H7 N O3) FORMUL 2 N2C 2(C5 H11 N O2 S) FORMUL 2 NCY 2(C4 H9 N O2 S) FORMUL 2 MVA 2(C6 H13 N O2) FORMUL 3 MG MG 2+ FORMUL 4 QUI 2(C9 H6 N2 O2) FORMUL 6 HOH *56(H2 O) LINK C QUI B 0 N DSN B 1 1555 1555 1.37 LINK C DSN B 1 N ALA B 2 1555 1555 1.34 LINK OG DSN B 1 C MVA B 8 1555 1555 1.33 LINK C ALA B 2 N BNCY B 3 1555 1555 1.35 LINK C ALA B 2 N AN2C B 3 1555 1555 1.35 LINK C AN2C B 3 N AMVA B 4 1555 1555 1.34 LINK C BNCY B 3 N BMVA B 4 1555 1555 1.33 LINK SG BNCY B 3 CB BN2C B 7 1555 1555 1.79 LINK CB AN2C B 3 SG ANCY B 7 1555 1555 1.81 LINK C BMVA B 4 OG BDSN B 5 1555 1555 1.32 LINK C AMVA B 4 OG ADSN B 5 1555 1555 1.31 LINK C DSN B 5 N ALA B 6 1555 1555 1.33 LINK N DSN B 5 C QUI B 9 1555 1555 1.36 LINK C ALA B 6 N ANCY B 7 1555 1555 1.34 LINK C ALA B 6 N BN2C B 7 1555 1555 1.34 LINK C ANCY B 7 N MVA B 8 1555 1555 1.32 LINK C BN2C B 7 N MVA B 8 1555 1555 1.32 LINK MG MG A 25 O HOH A2018 1555 1555 2.08 LINK MG MG A 25 O HOH A2018 1555 2665 2.08 LINK MG MG A 25 O HOH A2018 1555 3565 2.08 LINK MG MG A 25 O HOH A2020 1555 1555 2.10 LINK MG MG A 25 O HOH A2020 1555 2665 2.10 LINK MG MG A 25 O HOH A2020 1555 3565 2.10 SITE 1 AC1 2 HOH A2018 HOH A2020 SITE 1 AC2 13 DG A 1 DC A 2 DG A 3 DT A 4 SITE 2 AC2 13 DA A 5 DC A 6 DG A 7 DC A 8 SITE 3 AC2 13 HOH B2001 HOH B2003 HOH B2008 HOH B2009 SITE 4 AC2 13 HOH B2010 CRYST1 39.183 39.183 79.890 90.00 90.00 120.00 P 63 2 2 12 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 0.025521 0.014735 0.000000 0.00000 SCALE2 0.000000 0.029469 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012517 0.00000