HEADER ISOMERASE/DNA 09-JUN-04 1TL8
TITLE HUMAN DNA TOPOISOMERASE I (70 KDA) IN COMPLEX WITH THE
TITLE 2 INDENOISOQUINOLINE AI-III-52 AND COVALENT COMPLEX WITH A
TITLE 3 22 BASE PAIR DNA DUPLEX
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*TP*T)-3';
COMPND 3 CHAIN: B;
COMPND 4 ENGINEERED: YES;
COMPND 5 MOL_ID: 2;
COMPND 6 MOLECULE: 5'-D(*(TPC)P*GP*AP*AP*AP*AP*AP*TP*TP*TP*TP*T)-3';
COMPND 7 CHAIN: C;
COMPND 8 ENGINEERED: YES;
COMPND 9 MOL_ID: 3;
COMPND 10 MOLECULE: 5'-
COMPND 11 D(*AP*AP*AP*AP*AP*TP*TP*TP*TP*TP*CP*GP*AP*AP*GP*TP*CP*TP*TP
COMPND 12 *TP*TP*T)-3';
COMPND 13 CHAIN: D;
COMPND 14 ENGINEERED: YES;
COMPND 15 MOL_ID: 4;
COMPND 16 MOLECULE: DNA TOPOISOMERASE I;
COMPND 17 CHAIN: A;
COMPND 18 EC: 5.99.1.2;
COMPND 19 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 MOL_ID: 2;
SOURCE 4 SYNTHETIC: YES;
SOURCE 5 MOL_ID: 3;
SOURCE 6 SYNTHETIC: YES;
SOURCE 7 MOL_ID: 4;
SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 9 ORGANISM_COMMON: HUMAN;
SOURCE 10 ORGANISM_TAXID: 9606;
SOURCE 11 GENE: TOP1;
SOURCE 12 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA;
SOURCE 13 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM;
SOURCE 14 EXPRESSION_SYSTEM_TAXID: 7108;
SOURCE 15 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS
KEYWDS COMPLEX (ISOMERASE/DNA), DNA, TOPOISOMERASE I, DRUG, POISON,
KEYWDS 2 IDENOISOQUINOLINE
EXPDTA X-RAY DIFFRACTION
AUTHOR A.IOANOVICIU,S.ANTONY,Y.POMMIER,B.L.STAKER,L.STEWART,
AUTHOR 2 M.CUSHMAN
REVDAT 3 24-FEB-09 1TL8 1 VERSN
REVDAT 2 26-JUL-05 1TL8 1 JRNL
REVDAT 1 21-JUN-05 1TL8 0
JRNL AUTH A.IOANOVICIU,S.ANTONY,Y.POMMIER,B.L.STAKER,
JRNL AUTH 2 L.STEWART,M.CUSHMAN
JRNL TITL SYNTHESIS AND MECHANISM OF ACTION STUDIES OF A
JRNL TITL 2 SERIES OF NORINDENOISOQUINOLINE TOPOISOMERASE I
JRNL TITL 3 POISONS REVEAL AN INHIBITOR WITH A FLIPPED
JRNL TITL 4 ORIENTATION IN THE TERNARY DNA-ENZYME-INHIBITOR
JRNL TITL 5 COMPLEX AS DETERMINED BY X-RAY CRYSTALLOGRAPHIC
JRNL TITL 6 ANALYSIS
JRNL REF J.MED.CHEM. V. 48 4803 2005
JRNL REFN ISSN 0022-2623
JRNL PMID 16033260
JRNL DOI 10.1021/JM050076B
REMARK 1
REMARK 2
REMARK 2 RESOLUTION. 3.10 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CNX 2002
REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-
REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,
REMARK 3 : READ,RICE,SIMONSON,WARREN,ACCELRYS
REMARK 3 : SOFTWARE INC.(BADGER,BERARD,KUMAR,SZALMA,
REMARK 3 : YIP,DZAKULA)
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.10
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.57
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 947731.540
REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.8
REMARK 3 NUMBER OF REFLECTIONS : 16687
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING + TEST SET) : NULL
REMARK 3 R VALUE (WORKING SET) : 0.229
REMARK 3 FREE R VALUE : 0.305
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800
REMARK 3 FREE R VALUE TEST SET COUNT : 808
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.011
REMARK 3
REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA.
REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL
REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL
REMARK 3 FREE R VALUE (NO CUTOFF) : NULL
REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL
REMARK 3 ESTIMATED ERROR OF FREE R VALUE (NO CUTOFF) : NULL
REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 6
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.10
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.29
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.60
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2549
REMARK 3 BIN R VALUE (WORKING SET) : 0.3320
REMARK 3 BIN FREE R VALUE : 0.3950
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.00
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 106
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.038
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 4703
REMARK 3 NUCLEIC ACID ATOMS : 892
REMARK 3 HETEROGEN ATOMS : 24
REMARK 3 SOLVENT ATOMS : 0
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 60.40
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 60.40
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -19.82000
REMARK 3 B22 (A**2) : -9.32000
REMARK 3 B33 (A**2) : 29.14000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 13.09000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.37
REMARK 3 ESD FROM SIGMAA (A) : 0.47
REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00
REMARK 3
REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.52
REMARK 3 ESD FROM C-V SIGMAA (A) : 0.64
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.017
REMARK 3 BOND ANGLES (DEGREES) : 1.90
REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.80
REMARK 3 IMPROPER ANGLES (DEGREES) : 3.94
REMARK 3
REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
REMARK 3 MAIN-CHAIN BOND (A**2) : 2.670 ; 1.500
REMARK 3 MAIN-CHAIN ANGLE (A**2) : 4.550 ; 2.000
REMARK 3 SIDE-CHAIN BOND (A**2) : 3.700 ; 2.000
REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.730 ; 2.500
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED : FLAT MODEL
REMARK 3 KSOL : 0.27
REMARK 3 BSOL : 15.33
REMARK 3
REMARK 3 NCS MODEL : NULL
REMARK 3
REMARK 3 PARAMETER FILE 1 : PROTEIN.PARAM
REMARK 3 PARAMETER FILE 2 : DNA-RNA.PARAM
REMARK 3 PARAMETER FILE 3 : WATER_REP.PAR
REMARK 3 PARAMETER FILE 4 : ION.PAR
REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP
REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP
REMARK 3 TOPOLOGY FILE 3 : WATER_REP.TOP
REMARK 3 TOPOLOGY FILE 4 : ION.TOP
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1TL8 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JUL-04.
REMARK 100 THE RCSB ID CODE IS RCSB022744.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 03-DEC-03
REMARK 200 TEMPERATURE (KELVIN) : 100.0
REMARK 200 PH : 6.40
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : ALS
REMARK 200 BEAMLINE : 5.0.3
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.0
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16738
REMARK 200 RESOLUTION RANGE HIGH (A) : 3.100
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8
REMARK 200 DATA REDUNDANCY : 3.700
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.10000
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.7000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.10
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.21
REMARK 200 COMPLETENESS FOR SHELL (%) : 93.1
REMARK 200 DATA REDUNDANCY IN SHELL : 3.60
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : 0.52200
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.300
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: AMORE
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 56.56
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.83
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, MES, AMMONIUM SULFATE, PH
REMARK 280 6.40, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,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 57.07050
REMARK 290 SMTRY3 2 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: TETRAMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C, D, A
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 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 LYS A 174
REMARK 465 LYS A 175
REMARK 465 PRO A 176
REMARK 465 LYS A 177
REMARK 465 ASN A 178
REMARK 465 LYS A 179
REMARK 465 ASP A 180
REMARK 465 LYS A 181
REMARK 465 ASP A 182
REMARK 465 LYS A 183
REMARK 465 LYS A 184
REMARK 465 VAL A 185
REMARK 465 PRO A 186
REMARK 465 GLU A 187
REMARK 465 PRO A 188
REMARK 465 ASP A 189
REMARK 465 ASN A 190
REMARK 465 LYS A 191
REMARK 465 LYS A 192
REMARK 465 LYS A 193
REMARK 465 LYS A 194
REMARK 465 PRO A 195
REMARK 465 LYS A 196
REMARK 465 LYS A 197
REMARK 465 GLU A 198
REMARK 465 GLU A 199
REMARK 465 GLU A 200
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 D 114 C5 DA D 114 C6 -0.069
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 D 112 C3' - C2' - C1' ANGL. DEV. = -5.3 DEGREES
REMARK 500 LEU A 617 CA - CB - CG ANGL. DEV. = 16.4 DEGREES
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 LYS A 202 62.24 83.18
REMARK 500 PRO A 212 88.31 -56.59
REMARK 500 GLU A 213 121.77 4.74
REMARK 500 LYS A 223 12.96 -64.58
REMARK 500 PRO A 233 170.25 -47.98
REMARK 500 GLU A 236 -51.85 -8.10
REMARK 500 VAL A 238 79.93 -109.91
REMARK 500 THR A 269 4.40 -66.62
REMARK 500 THR A 287 -169.48 -76.95
REMARK 500 ALA A 315 42.82 -95.01
REMARK 500 ARG A 316 -43.23 -131.36
REMARK 500 LYS A 321 -10.96 -49.97
REMARK 500 ASP A 344 76.47 51.54
REMARK 500 ASN A 345 -3.38 76.06
REMARK 500 ALA A 351 -77.36 -52.22
REMARK 500 ARG A 362 -46.28 -133.81
REMARK 500 ASN A 366 49.53 -79.63
REMARK 500 GLU A 403 149.88 -170.68
REMARK 500 ASP A 407 93.53 -51.74
REMARK 500 ARG A 458 1.72 -69.91
REMARK 500 SER A 467 133.60 -1.46
REMARK 500 TYR A 523 69.00 66.11
REMARK 500 SER A 534 15.75 59.51
REMARK 500 GLU A 556 121.65 -38.65
REMARK 500 PRO A 637 122.49 -36.21
REMARK 500 LYS A 638 91.00 -37.23
REMARK 500 GLU A 641 31.96 -96.44
REMARK 500 MET A 675 101.81 86.13
REMARK 500 THR A 680 -58.67 -158.04
REMARK 500 ASN A 711 40.41 -103.76
REMARK 500 ASN A 745 -170.35 -69.46
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 B 8 0.07 SIDE_CHAIN
REMARK 500 DT B 10 0.06 SIDE_CHAIN
REMARK 500 DA D 102 0.06 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 AI3 D 901
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1K4T RELATED DB: PDB
REMARK 900 HUMAN DNA TOPOISOMERASE I (70 KDA) IN COMPLEX WITH THE
REMARK 900 POISON TOPOTECAN AND COVALENT COMPLEX WITH A 22 BASE PAIR
REMARK 900 DNA DUPLEX
DBREF 1TL8 A 174 765 UNP P11387 TOP1_HUMAN 174 765
DBREF 1TL8 B 1 10 PDB 1TL8 1TL8 1 10
DBREF 1TL8 C 11 22 PDB 1TL8 1TL8 11 22
DBREF 1TL8 D 101 122 PDB 1TL8 1TL8 101 122
SEQADV 1TL8 PTR A 723 UNP P11387 TYR 723 MODIFIED RESIDUE
SEQRES 1 B 10 DA DA DA DA DA DG DA DC DT DT
SEQRES 1 C 12 TPC DG DA DA DA DA DA DT DT DT DT DT
SEQRES 1 D 22 DA DA DA DA DA DT DT DT DT DT DC DG DA
SEQRES 2 D 22 DA DG DT DC DT DT DT DT DT
SEQRES 1 A 592 LYS LYS PRO LYS ASN LYS ASP LYS ASP LYS LYS VAL PRO
SEQRES 2 A 592 GLU PRO ASP ASN LYS LYS LYS LYS PRO LYS LYS GLU GLU
SEQRES 3 A 592 GLU GLN LYS TRP LYS TRP TRP GLU GLU GLU ARG TYR PRO
SEQRES 4 A 592 GLU GLY ILE LYS TRP LYS PHE LEU GLU HIS LYS GLY PRO
SEQRES 5 A 592 VAL PHE ALA PRO PRO TYR GLU PRO LEU PRO GLU ASN VAL
SEQRES 6 A 592 LYS PHE TYR TYR ASP GLY LYS VAL MET LYS LEU SER PRO
SEQRES 7 A 592 LYS ALA GLU GLU VAL ALA THR PHE PHE ALA LYS MET LEU
SEQRES 8 A 592 ASP HIS GLU TYR THR THR LYS GLU ILE PHE ARG LYS ASN
SEQRES 9 A 592 PHE PHE LYS ASP TRP ARG LYS GLU MET THR ASN GLU GLU
SEQRES 10 A 592 LYS ASN ILE ILE THR ASN LEU SER LYS CYS ASP PHE THR
SEQRES 11 A 592 GLN MET SER GLN TYR PHE LYS ALA GLN THR GLU ALA ARG
SEQRES 12 A 592 LYS GLN MET SER LYS GLU GLU LYS LEU LYS ILE LYS GLU
SEQRES 13 A 592 GLU ASN GLU LYS LEU LEU LYS GLU TYR GLY PHE CYS ILE
SEQRES 14 A 592 MET ASP ASN HIS LYS GLU ARG ILE ALA ASN PHE LYS ILE
SEQRES 15 A 592 GLU PRO PRO GLY LEU PHE ARG GLY ARG GLY ASN HIS PRO
SEQRES 16 A 592 LYS MET GLY MET LEU LYS ARG ARG ILE MET PRO GLU ASP
SEQRES 17 A 592 ILE ILE ILE ASN CYS SER LYS ASP ALA LYS VAL PRO SER
SEQRES 18 A 592 PRO PRO PRO GLY HIS LYS TRP LYS GLU VAL ARG HIS ASP
SEQRES 19 A 592 ASN LYS VAL THR TRP LEU VAL SER TRP THR GLU ASN ILE
SEQRES 20 A 592 GLN GLY SER ILE LYS TYR ILE MET LEU ASN PRO SER SER
SEQRES 21 A 592 ARG ILE LYS GLY GLU LYS ASP TRP GLN LYS TYR GLU THR
SEQRES 22 A 592 ALA ARG ARG LEU LYS LYS CYS VAL ASP LYS ILE ARG ASN
SEQRES 23 A 592 GLN TYR ARG GLU ASP TRP LYS SER LYS GLU MET LYS VAL
SEQRES 24 A 592 ARG GLN ARG ALA VAL ALA LEU TYR PHE ILE ASP LYS LEU
SEQRES 25 A 592 ALA LEU ARG ALA GLY ASN GLU LYS GLU GLU GLY GLU THR
SEQRES 26 A 592 ALA ASP THR VAL GLY CYS CYS SER LEU ARG VAL GLU HIS
SEQRES 27 A 592 ILE ASN LEU HIS PRO GLU LEU ASP GLY GLN GLU TYR VAL
SEQRES 28 A 592 VAL GLU PHE ASP PHE LEU GLY LYS ASP SER ILE ARG TYR
SEQRES 29 A 592 TYR ASN LYS VAL PRO VAL GLU LYS ARG VAL PHE LYS ASN
SEQRES 30 A 592 LEU GLN LEU PHE MET GLU ASN LYS GLN PRO GLU ASP ASP
SEQRES 31 A 592 LEU PHE ASP ARG LEU ASN THR GLY ILE LEU ASN LYS HIS
SEQRES 32 A 592 LEU GLN ASP LEU MET GLU GLY LEU THR ALA LYS VAL PHE
SEQRES 33 A 592 ARG THR TYR ASN ALA SER ILE THR LEU GLN GLN GLN LEU
SEQRES 34 A 592 LYS GLU LEU THR ALA PRO ASP GLU ASN ILE PRO ALA LYS
SEQRES 35 A 592 ILE LEU SER TYR ASN ARG ALA ASN ARG ALA VAL ALA ILE
SEQRES 36 A 592 LEU CYS ASN HIS GLN ARG ALA PRO PRO LYS THR PHE GLU
SEQRES 37 A 592 LYS SER MET MET ASN LEU GLN THR LYS ILE ASP ALA LYS
SEQRES 38 A 592 LYS GLU GLN LEU ALA ASP ALA ARG ARG ASP LEU LYS SER
SEQRES 39 A 592 ALA LYS ALA ASP ALA LYS VAL MET LYS ASP ALA LYS THR
SEQRES 40 A 592 LYS LYS VAL VAL GLU SER LYS LYS LYS ALA VAL GLN ARG
SEQRES 41 A 592 LEU GLU GLU GLN LEU MET LYS LEU GLU VAL GLN ALA THR
SEQRES 42 A 592 ASP ARG GLU GLU ASN LYS GLN ILE ALA LEU GLY THR SER
SEQRES 43 A 592 LYS LEU ASN PTR LEU ASP PRO ARG ILE THR VAL ALA TRP
SEQRES 44 A 592 CYS LYS LYS TRP GLY VAL PRO ILE GLU LYS ILE TYR ASN
SEQRES 45 A 592 LYS THR GLN ARG GLU LYS PHE ALA TRP ALA ILE ASP MET
SEQRES 46 A 592 ALA ASP GLU ASP TYR GLU PHE
MODRES 1TL8 TPC C 11 DC
MODRES 1TL8 PTR A 723 TYR O-PHOSPHOTYROSINE
HET TPC C 11 16
HET PTR A 723 16
HET AI3 D 901 24
HETNAM TPC 5'-THIO-2'-DEOXY-CYTOSINE PHOSPHONIC ACID
HETNAM PTR O-PHOSPHOTYROSINE
HETNAM AI3 2,3-DIMETHOXY-12H-[1,3]DIOXOLO[5,6]INDENO[1,2-
HETNAM 2 AI3 C]ISOQUINOLIN-6-IUM
HETSYN PTR PHOSPHONOTYROSINE
HETSYN AI3 AI-III-52
FORMUL 2 TPC C9 H14 N3 O6 P S
FORMUL 4 PTR C9 H12 N O6 P
FORMUL 5 AI3 C19 H16 N O4 1+
HELIX 1 1 SER A 250 LEU A 264 1 15
HELIX 2 2 ASP A 265 THR A 270 5 6
HELIX 3 3 LYS A 271 GLU A 285 1 15
HELIX 4 4 THR A 287 ILE A 294 1 8
HELIX 5 5 PHE A 302 ALA A 315 1 14
HELIX 6 6 SER A 320 TYR A 338 1 19
HELIX 7 7 MET A 378 GLU A 380 5 3
HELIX 8 8 SER A 433 CYS A 453 1 21
HELIX 9 9 CYS A 453 ASP A 464 1 12
HELIX 10 10 GLU A 469 ALA A 486 1 18
HELIX 11 11 ARG A 508 GLU A 510 5 3
HELIX 12 12 GLY A 531 ILE A 535 5 5
HELIX 13 13 GLU A 544 GLU A 556 1 13
HELIX 14 14 ASN A 569 MET A 581 1 13
HELIX 15 15 LYS A 587 GLU A 604 1 18
HELIX 16 16 ASN A 611 CYS A 630 1 20
HELIX 17 17 LYS A 650 ASP A 664 1 15
HELIX 18 18 ASP A 664 LYS A 669 1 6
HELIX 19 19 LYS A 688 GLU A 710 1 23
HELIX 20 20 LEU A 716 ASN A 722 1 7
HELIX 21 21 ASP A 725 TRP A 736 1 12
HELIX 22 22 PRO A 739 ILE A 743 5 5
HELIX 23 23 ASN A 745 PHE A 752 1 8
HELIX 24 24 PHE A 752 ALA A 759 1 8
SHEET 1 A 3 LEU A 220 GLU A 221 0
SHEET 2 A 3 PHE A 340 MET A 343 -1 O ILE A 342 N GLU A 221
SHEET 3 A 3 LYS A 347 ARG A 349 -1 O GLU A 348 N CYS A 341
SHEET 1 B 3 LYS A 245 MET A 247 0
SHEET 2 B 3 PHE A 240 TYR A 242 -1 N PHE A 240 O MET A 247
SHEET 3 B 3 CYS A 300 ASP A 301 -1 O ASP A 301 N TYR A 241
SHEET 1 C 4 GLU A 403 ARG A 405 0
SHEET 2 C 4 ILE A 382 ASN A 385 1 N ILE A 384 O ARG A 405
SHEET 3 C 4 VAL A 414 THR A 417 -1 O SER A 415 N ILE A 383
SHEET 4 C 4 ILE A 424 ILE A 427 -1 O ILE A 427 N VAL A 414
SHEET 1 D 3 ILE A 512 LEU A 518 0
SHEET 2 D 3 GLN A 521 PHE A 527 -1 O GLU A 526 N ASN A 513
SHEET 3 D 3 ASN A 539 PRO A 542 -1 O ASN A 539 N PHE A 527
LINK C3' DT B 10 O3P PTR A 723 1555 1555 1.43
LINK O3' TPC C 11 P DG C 12 1555 1555 1.62
LINK C ASN A 722 N PTR A 723 1555 1555 1.32
LINK C PTR A 723 N LEU A 724 1555 1555 1.34
SITE 1 AC1 7 ARG A 364 THR A 718 ASN A 722 DT B 10
SITE 2 AC1 7 TPC C 11 DG D 112 DA D 113
CRYST1 56.949 114.141 73.499 90.00 94.18 90.00 P 1 21 1 2
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 0.017560 0.000000 0.001282 0.00000
SCALE2 0.000000 0.008761 0.000000 0.00000
SCALE3 0.000000 0.000000 0.013642 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
