PDB Short entry for 1SEU HEADER ISOMERASE/DNA 18-FEB-04 1SEU TITLE HUMAN DNA TOPOISOMERASE I (70 KDA) IN COMPLEX WITH THE INDOLOCARBAZOLE TITLE 2 SA315F AND COVALENT COMPLEX WITH A 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(*(TGP)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'-D(*AP*AP*AP*AP*AP*TP*TP*TP*TP*TP*CP*CP*AP*AP*GP*TP*CP*TP COMPND 11 *TP*TP*TP*T)-3'; COMPND 12 CHAIN: D; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 4; COMPND 15 MOLECULE: DNA TOPOISOMERASE I; COMPND 16 CHAIN: A; COMPND 17 EC: 5.99.1.2; COMPND 18 ENGINEERED: YES; COMPND 19 MUTATION: 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_CELL_LINE: SF9; SOURCE 16 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 17 EXPRESSION_SYSTEM_PLASMID: PFACTBAC1 KEYWDS COMPLEX (ISOMERASE-DNA), DNA, TOPOISOMERASE I, DRUG, POISON, KEYWDS 2 ISOMERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.L.STAKER,M.D.FEESE,M.CUSHMAN,Y.POMMIER,D.ZEMBOWER,L.STEWART, AUTHOR 2 A.B.BURGIN REVDAT 6 15-NOV-23 1SEU 1 REMARK REVDAT 5 23-AUG-23 1SEU 1 REMARK REVDAT 4 27-OCT-21 1SEU 1 REMARK SEQADV LINK REVDAT 3 24-FEB-09 1SEU 1 VERSN REVDAT 2 10-MAY-05 1SEU 1 REMARK SEQRES COMPND REVDAT 1 19-APR-05 1SEU 0 JRNL AUTH B.L.STAKER,M.D.FEESE,M.CUSHMAN,Y.POMMIER,D.ZEMBOWER, JRNL AUTH 2 L.STEWART,A.B.BURGIN JRNL TITL STRUCTURES OF THREE CLASSES OF ANTICANCER AGENTS BOUND TO JRNL TITL 2 THE HUMAN TOPOISOMERASE I-DNA COVALENT COMPLEX JRNL REF J.MED.CHEM. V. 48 2336 2005 JRNL REFN ISSN 0022-2623 JRNL PMID 15801827 JRNL DOI 10.1021/JM049146P REMARK 2 REMARK 2 RESOLUTION. 3.00 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) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.63 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1701025.160 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 80.4 REMARK 3 NUMBER OF REFLECTIONS : 15516 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) : 0.237 REMARK 3 R VALUE (WORKING SET) : 0.237 REMARK 3 FREE R VALUE : 0.295 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1575 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 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) : 3.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.19 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 38.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1127 REMARK 3 BIN R VALUE (WORKING SET) : 0.3570 REMARK 3 BIN FREE R VALUE : 0.3930 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 112 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.037 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4685 REMARK 3 NUCLEIC ACID ATOMS : 892 REMARK 3 HETEROGEN ATOMS : 38 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 78.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -19.35000 REMARK 3 B22 (A**2) : -28.08000 REMARK 3 B33 (A**2) : 47.43000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 9.80000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.40 REMARK 3 ESD FROM SIGMAA (A) : 0.55 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) : 0.50 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.59 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 3.700 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) : 1.820 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.170 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.260 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.680 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.24 REMARK 3 BSOL : 10.00 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 : PROTEIN.PARAM REMARK 3 PARAMETER FILE 2 : DNA-RNA.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PAR REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : SA3_PAR.PAR REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.PARAM REMARK 3 TOPOLOGY FILE 5 : SA3_TOP.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1SEU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-APR-04. REMARK 100 THE DEPOSITION ID IS D_1000021644. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUL-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 32-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15533 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 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 (%) : 80.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.10700 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 38.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.32500 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.500 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: 1K4T REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, AMMONIUM SULFATE, MES, PH REMARK 280 6.4, 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 57.98250 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 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 GLN A 201 CG CD OE1 NE2 REMARK 470 LYS A 202 CG CD CE NZ REMARK 470 THR A 639 OG1 CG2 REMARK 470 PHE A 640 CG CD1 CD2 CE1 CE2 CZ 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 LEU A 617 CA - CB - CG ANGL. DEV. = 16.6 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 202 111.14 69.96 REMARK 500 ASP A 344 83.30 59.98 REMARK 500 ARG A 362 -41.70 -131.99 REMARK 500 PRO A 397 120.72 -36.63 REMARK 500 CYS A 453 23.90 -143.04 REMARK 500 ASP A 483 -71.07 -69.80 REMARK 500 ALA A 486 78.27 60.89 REMARK 500 ASP A 519 28.21 49.24 REMARK 500 VAL A 543 -166.60 -101.45 REMARK 500 ASN A 557 29.96 46.73 REMARK 500 ASN A 569 -157.59 -151.17 REMARK 500 ASN A 631 71.61 44.21 REMARK 500 HIS A 632 51.89 -115.97 REMARK 500 LYS A 638 109.60 -52.28 REMARK 500 THR A 639 3.98 58.68 REMARK 500 MET A 675 93.17 68.69 REMARK 500 ASP A 757 -74.50 -85.32 REMARK 500 ALA A 759 116.35 169.43 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 TYR A 592 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 ATOM O3* OF THYMINE 10, CHAIN B IS MISSING REMARK 600 DUE TO THE COVALENT BOND FORMED BETWEEN REMARK 600 THYMINE 10 AND PHOSPHOTYROSINE (PTR) 723 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SA3 D 990 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1SC7 RELATED DB: PDB REMARK 900 HUMAN DNA TOPOISOMERASE I (70 KDA) IN COMPLEX WITH THE REMARK 900 INDENOISOQUINOLINE MJ-II-38 AND COVALENT COMPLEX WITH A 22 BASE REMARK 900 PAIR DNA DUPLEX REMARK 900 RELATED ID: 1K4T RELATED DB: PDB REMARK 900 HUMAN DNA TOPOISOMERASE I (70 KDA) IN COMPLEX WITH THE POISON REMARK 900 TOPOTECAN AND COVALENT COMPLEX WITH A 22 BASE PAIR DNA DUPLEX DBREF 1SEU A 174 765 UNP P11387 TOP1_HUMAN 174 765 DBREF 1SEU B 1 10 PDB 1SEU 1SEU 1 10 DBREF 1SEU C 11 22 PDB 1SEU 1SEU 11 22 DBREF 1SEU D 101 122 PDB 1SEU 1SEU 101 122 SEQADV 1SEU SER A 722 UNP P11387 ASN 722 ENGINEERED MUTATION SEQADV 1SEU 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 TGP 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 DC 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 SER 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 1SEU TGP C 11 DG MODRES 1SEU PTR A 723 TYR O-PHOSPHOTYROSINE HET TGP C 11 19 HET PTR A 723 16 HET SA3 D 990 38 HETNAM TGP 5'-THIO-2'-DEOXY-GUANOSINE PHOSPHONIC ACID HETNAM PTR O-PHOSPHOTYROSINE HETNAM SA3 2,10-DIHYDROXY-12-(BETA-D-GLUCOPYRANOSYL)-6,7,12,13- HETNAM 2 SA3 TETRAHYDROINDOLO[2,3-A]PYRROLO[3,4-C]CARBAZOLE-5,7- HETNAM 3 SA3 DIONE HETSYN PTR PHOSPHONOTYROSINE FORMUL 2 TGP C10 H14 N5 O6 P S FORMUL 4 PTR C9 H12 N O6 P FORMUL 5 SA3 C26 H21 N3 O9 HELIX 1 1 LYS A 204 GLU A 208 5 5 HELIX 2 2 LYS A 252 LYS A 262 1 11 HELIX 3 3 GLU A 267 THR A 270 5 4 HELIX 4 4 LYS A 271 GLU A 285 1 15 HELIX 5 5 PHE A 302 GLN A 318 1 17 HELIX 6 6 SER A 320 ASN A 331 1 12 HELIX 7 7 LYS A 333 TYR A 338 1 6 HELIX 8 8 MET A 378 ASP A 381 5 4 HELIX 9 9 SER A 433 THR A 446 1 14 HELIX 10 10 ALA A 447 LYS A 452 1 6 HELIX 11 11 CYS A 453 ASN A 459 1 7 HELIX 12 12 ARG A 462 SER A 467 5 6 HELIX 13 13 GLU A 469 LYS A 484 1 16 HELIX 14 14 GLY A 503 LEU A 507 5 5 HELIX 15 15 ARG A 508 GLU A 510 5 3 HELIX 16 16 LYS A 532 SER A 534 5 3 HELIX 17 17 GLU A 544 LYS A 549 1 6 HELIX 18 18 LYS A 549 MET A 555 1 7 HELIX 19 19 ASN A 569 ASP A 579 1 11 HELIX 20 20 LYS A 587 THR A 606 1 20 HELIX 21 21 ASN A 611 CYS A 630 1 20 HELIX 22 22 SER A 643 THR A 649 1 7 HELIX 23 23 ALA A 653 ALA A 659 1 7 HELIX 24 24 ALA A 661 LYS A 666 1 6 HELIX 25 25 LYS A 682 LYS A 687 1 6 HELIX 26 26 LYS A 688 ASN A 711 1 24 HELIX 27 27 LEU A 716 PTR A 723 1 8 HELIX 28 28 ASP A 725 TRP A 736 1 12 HELIX 29 29 PRO A 739 ILE A 743 5 5 HELIX 30 30 ASN A 745 PHE A 752 1 8 HELIX 31 31 PHE A 752 MET A 758 1 7 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 TYR A 242 O LYS A 245 SHEET 3 B 3 CYS A 300 ASP A 301 -1 O ASP A 301 N TYR A 241 SHEET 1 C 2 GLY A 359 LEU A 360 0 SHEET 2 C 2 LEU A 373 LYS A 374 -1 O LYS A 374 N GLY A 359 SHEET 1 D 4 GLU A 403 ARG A 405 0 SHEET 2 D 4 ILE A 383 ASN A 385 1 N ILE A 384 O ARG A 405 SHEET 3 D 4 VAL A 414 THR A 417 -1 O SER A 415 N ILE A 383 SHEET 4 D 4 ILE A 424 ILE A 427 -1 O LYS A 425 N TRP A 416 SHEET 1 E 3 ILE A 512 LEU A 518 0 SHEET 2 E 3 GLN A 521 LEU A 530 -1 O GLU A 526 N ASN A 513 SHEET 3 E 3 ARG A 536 PRO A 542 -1 O TYR A 537 N PHE A 529 LINK C3' DT B 10 O3P PTR A 723 1555 1555 1.42 LINK O3' TGP C 11 P DG C 12 1555 1555 1.60 LINK C SER A 722 N PTR A 723 1555 1555 1.34 LINK C PTR A 723 N LEU A 724 1555 1555 1.33 SITE 1 AC1 7 ASN A 352 ARG A 364 SER A 722 DT B 10 SITE 2 AC1 7 TGP C 11 DC D 112 DA D 113 CRYST1 57.382 115.965 73.547 90.00 93.71 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 0.017427 0.000000 0.001130 0.00000 SCALE2 0.000000 0.008623 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013625 0.00000