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 22 BASE PAIR TITLE 3 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'-D(*AP*AP*AP*AP*AP*TP*TP*TP*TP*TP*CP*GP*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 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, ISOMERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.IOANOVICIU,S.ANTONY,Y.POMMIER,B.L.STAKER,L.STEWART,M.CUSHMAN REVDAT 4 06-NOV-24 1TL8 1 REMARK SEQADV LINK 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,L.STEWART, JRNL AUTH 2 M.CUSHMAN JRNL TITL SYNTHESIS AND MECHANISM OF ACTION STUDIES OF A SERIES OF JRNL TITL 2 NORINDENOISOQUINOLINE TOPOISOMERASE I POISONS REVEAL AN JRNL TITL 3 INHIBITOR WITH A FLIPPED ORIENTATION IN THE TERNARY JRNL TITL 4 DNA-ENZYME-INHIBITOR COMPLEX AS DETERMINED BY X-RAY JRNL TITL 5 CRYSTALLOGRAPHIC ANALYSIS JRNL REF J.MED.CHEM. V. 48 4803 2005 JRNL REFN ISSN 0022-2623 JRNL PMID 16033260 JRNL DOI 10.1021/JM050076B 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) : 0.229 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) : 1.900 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 3.940 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 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.PAR REMARK 3 PARAMETER FILE 5 : NULL 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 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1TL8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JUL-04. REMARK 100 THE DEPOSITION ID IS D_1000022744. 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 LEU A 724 102.32 65.52 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 POISON REMARK 900 TOPOTECAN AND COVALENT COMPLEX WITH A 22 BASE PAIR 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