PDB Short entry for 1LPQ HEADER ISOMERASE/DNA 08-MAY-02 1LPQ TITLE HUMAN DNA TOPOISOMERASE I (70 KDA) IN NON-COVALENT COMPLEX WITH A 22 TITLE 2 BASE PAIR DNA DUPLEX CONTAINING AN 8-OXOG LESION COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*TP*TP*(8OG) COMPND 3 P*GP*AP*AP*AP*AP*AP*TP*TP*TP*TP*T)-3'; COMPND 4 CHAIN: B; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-D(*AP*AP*AP*AP*AP*TP*TP*TP*TP*TP*CP*CP*AP*AP*GP*TP*CP*TP COMPND 8 *TP*TP*TP*T)-3'; COMPND 9 CHAIN: C; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA TOPOISOMERASE I; COMPND 13 CHAIN: A; COMPND 14 EC: 5.99.1.2; COMPND 15 ENGINEERED: YES; COMPND 16 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 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 7 ORGANISM_COMMON: HUMAN; SOURCE 8 ORGANISM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 10 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 12 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS KEYWDS PROTEIN-DNA COMPLEX, DNA DAMAGE, INDUCED CONFORMATIONAL CHANGE, KEYWDS 2 ISOMERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR D.T.LESHER,Y.POMMIER,L.STEWART,M.R.REDINBO REVDAT 5 14-FEB-24 1LPQ 1 REMARK REVDAT 4 27-OCT-21 1LPQ 1 SEQADV LINK REVDAT 3 24-FEB-09 1LPQ 1 VERSN REVDAT 2 25-SEP-02 1LPQ 1 JRNL REVDAT 1 16-AUG-02 1LPQ 0 JRNL AUTH D.T.LESHER,Y.POMMIER,L.STEWART,M.R.REDINBO JRNL TITL 8-OXOGUANINE REARRANGES THE ACTIVE SITE OF HUMAN JRNL TITL 2 TOPOISOMERASE I JRNL REF PROC.NATL.ACAD.SCI.USA V. 99 12102 2002 JRNL REFN ISSN 0027-8424 JRNL PMID 12209008 JRNL DOI 10.1073/PNAS.192282699 REMARK 2 REMARK 2 RESOLUTION. 3.14 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.14 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.87 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 16401 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 SET) : 0.256 REMARK 3 FREE R VALUE : 0.298 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1132 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 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) : 3.14 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.34 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2380 REMARK 3 BIN R VALUE (WORKING SET) : 0.3600 REMARK 3 BIN FREE R VALUE : 0.3910 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 7.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 184 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.029 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4457 REMARK 3 NUCLEIC ACID ATOMS : 897 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 27 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 64.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.68000 REMARK 3 B22 (A**2) : 8.89000 REMARK 3 B33 (A**2) : -4.21000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 13.32000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.43 REMARK 3 ESD FROM SIGMAA (A) : 0.41 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) : 0.54 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.55 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.020 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) : 1.260 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.260 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 10.600; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 12.710; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1LPQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-MAY-02. REMARK 100 THE DEPOSITION ID IS D_1000016164. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X12B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.10 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRANDEIS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17165 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.140 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.700 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : 0.33400 REMARK 200 R SYM (I) : 0.20000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.14 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.19 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.5 REMARK 200 DATA REDUNDANCY IN SHELL : 1.80 REMARK 200 R MERGE FOR SHELL (I) : 0.30000 REMARK 200 R SYM FOR SHELL (I) : 0.26500 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.700 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 (%): 60.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TRIS-HCL, MES, PEG 400, MAGNESIUM REMARK 280 CHLORIDE, DITHIOTHREITOL, PH 6.8, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 295K 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 61.25000 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C, 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 ARG A 634 REMARK 465 ALA A 635 REMARK 465 PRO A 636 REMARK 465 PRO A 637 REMARK 465 LYS A 638 REMARK 465 THR A 639 REMARK 465 PHE A 640 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 GLU A 213 CG CD OE1 OE2 REMARK 470 LYS A 248 CG CD CE NZ REMARK 470 LYS A 276 CG CD CE NZ REMARK 470 GLU A 289 CG CD OE1 OE2 REMARK 470 GLN A 304 CG CD OE1 NE2 REMARK 470 GLU A 314 CG CD OE1 OE2 REMARK 470 ARG A 316 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 317 CG CD CE NZ REMARK 470 GLN A 318 CG CD OE1 NE2 REMARK 470 MET A 319 CG SD CE REMARK 470 LYS A 321 CG CD CE NZ REMARK 470 GLU A 322 CG CD OE1 OE2 REMARK 470 GLU A 323 CG CD OE1 OE2 REMARK 470 LYS A 326 CG CD CE NZ REMARK 470 GLU A 329 CG CD OE1 OE2 REMARK 470 GLU A 332 CG CD OE1 OE2 REMARK 470 LYS A 333 CG CD CE NZ REMARK 470 ARG A 362 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 463 CG CD OE1 OE2 REMARK 470 LYS A 466 CG CD CE NZ REMARK 470 LYS A 468 CG CD CE NZ REMARK 470 LYS A 471 CG CD CE NZ REMARK 470 LYS A 484 CG CD CE NZ REMARK 470 GLU A 494 CG CD OE1 OE2 REMARK 470 GLU A 495 CG CD OE1 OE2 REMARK 470 ARG A 546 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 582 CG CD OE1 OE2 REMARK 470 ASP A 609 CG OD1 OD2 REMARK 470 GLU A 610 CG CD OE1 OE2 REMARK 470 ASN A 611 CG OD1 ND2 REMARK 470 GLN A 633 CG CD OE1 NE2 REMARK 470 GLU A 641 CG CD OE1 OE2 REMARK 470 LYS A 642 CG CD CE NZ REMARK 470 SER A 643 OG REMARK 470 MET A 645 CG SD CE REMARK 470 ASN A 646 CG OD1 ND2 REMARK 470 ASP A 660 CG OD1 OD2 REMARK 470 VAL A 674 CG1 CG2 REMARK 470 GLU A 696 CG CD OE1 OE2 REMARK 470 LYS A 712 CG CD CE NZ REMARK 470 LYS A 735 CG CD CE NZ REMARK 470 GLU A 741 CG CD OE1 OE2 REMARK 470 LYS A 742 CG CD CE NZ REMARK 470 ASP A 760 CG OD1 OD2 REMARK 470 GLU A 764 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O VAL A 414 O TYR A 426 2.13 REMARK 500 O GLN A 460 OD1 ASP A 464 2.16 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 DC C 112 C3' - C2' - C1' ANGL. DEV. = -5.0 DEGREES REMARK 500 VAL A 472 N - CA - C ANGL. DEV. = -18.9 DEGREES REMARK 500 ASP A 664 N - CA - C ANGL. DEV. = -21.0 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 PHE A 227 172.66 -52.22 REMARK 500 PRO A 251 -71.60 -33.90 REMARK 500 LYS A 262 -8.03 -58.77 REMARK 500 ASN A 296 -24.26 -147.17 REMARK 500 LEU A 297 -12.86 76.21 REMARK 500 GLN A 318 77.36 -176.70 REMARK 500 LYS A 324 -76.64 -58.54 REMARK 500 LEU A 325 -14.76 -49.27 REMARK 500 ASP A 344 85.47 41.14 REMARK 500 ASN A 345 19.40 53.47 REMARK 500 ASN A 366 45.90 -66.09 REMARK 500 PRO A 379 -18.84 -45.50 REMARK 500 ASN A 385 -81.19 -109.19 REMARK 500 CYS A 386 172.13 40.82 REMARK 500 PRO A 396 152.28 -44.07 REMARK 500 PRO A 397 114.64 -38.15 REMARK 500 GLU A 403 145.88 -171.13 REMARK 500 SER A 415 138.58 -179.38 REMARK 500 SER A 423 -165.79 -108.89 REMARK 500 TYR A 426 -70.42 -119.80 REMARK 500 ILE A 427 104.70 92.54 REMARK 500 ARG A 434 11.52 -68.99 REMARK 500 LYS A 452 -68.63 -96.30 REMARK 500 CYS A 453 36.04 -81.16 REMARK 500 GLN A 460 -82.86 -76.10 REMARK 500 TYR A 461 -19.64 -48.56 REMARK 500 GLU A 463 32.55 -85.54 REMARK 500 LYS A 468 -32.51 -39.42 REMARK 500 LYS A 471 -179.65 -57.53 REMARK 500 VAL A 472 -149.65 57.31 REMARK 500 ARG A 473 83.59 3.71 REMARK 500 GLN A 474 -49.77 152.52 REMARK 500 ALA A 486 59.47 36.71 REMARK 500 ALA A 489 -75.25 -28.57 REMARK 500 GLU A 494 107.13 -56.20 REMARK 500 ASP A 519 43.04 24.61 REMARK 500 TYR A 523 88.26 59.41 REMARK 500 ASP A 533 -8.52 64.79 REMARK 500 SER A 534 22.12 90.15 REMARK 500 ASN A 539 107.12 176.28 REMARK 500 PHE A 554 45.91 -76.98 REMARK 500 ASN A 557 37.04 70.06 REMARK 500 PHE A 565 54.58 -116.12 REMARK 500 ARG A 567 31.56 77.99 REMARK 500 ALA A 586 -56.81 -15.19 REMARK 500 VAL A 588 -32.32 -38.77 REMARK 500 GLN A 600 -82.88 -79.59 REMARK 500 GLN A 601 -41.32 -23.97 REMARK 500 LYS A 603 14.79 -64.42 REMARK 500 LEU A 605 13.08 -148.26 REMARK 500 REMARK 500 THIS ENTRY HAS 82 RAMACHANDRAN OUTLIERS. 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 C 112 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1A31 RELATED DB: PDB REMARK 900 RELATED ID: 1A35 RELATED DB: PDB REMARK 900 RELATED ID: 1A36 RELATED DB: PDB REMARK 900 RELATED ID: 1EJ9 RELATED DB: PDB DBREF 1LPQ A 202 765 UNP P11387 TOP1_HUMAN 202 765 DBREF 1LPQ B 1 22 PDB 1LPQ 1LPQ 1 22 DBREF 1LPQ C 101 122 PDB 1LPQ 1LPQ 101 122 SEQADV 1LPQ PHE A 723 UNP P11387 TYR 723 ENGINEERED MUTATION SEQRES 1 B 22 DA DA DA DA DA DG DA DC DT DT 8OG DG DA SEQRES 2 B 22 DA DA DA DA DT DT DT DT DT SEQRES 1 C 22 DA DA DA DA DA DT DT DT DT DT DC DC DA SEQRES 2 C 22 DA DG DT DC DT DT DT DT DT SEQRES 1 A 564 LYS TRP LYS TRP TRP GLU GLU GLU ARG TYR PRO GLU GLY SEQRES 2 A 564 ILE LYS TRP LYS PHE LEU GLU HIS LYS GLY PRO VAL PHE SEQRES 3 A 564 ALA PRO PRO TYR GLU PRO LEU PRO GLU ASN VAL LYS PHE SEQRES 4 A 564 TYR TYR ASP GLY LYS VAL MET LYS LEU SER PRO LYS ALA SEQRES 5 A 564 GLU GLU VAL ALA THR PHE PHE ALA LYS MET LEU ASP HIS SEQRES 6 A 564 GLU TYR THR THR LYS GLU ILE PHE ARG LYS ASN PHE PHE SEQRES 7 A 564 LYS ASP TRP ARG LYS GLU MET THR ASN GLU GLU LYS ASN SEQRES 8 A 564 ILE ILE THR ASN LEU SER LYS CYS ASP PHE THR GLN MET SEQRES 9 A 564 SER GLN TYR PHE LYS ALA GLN THR GLU ALA ARG LYS GLN SEQRES 10 A 564 MET SER LYS GLU GLU LYS LEU LYS ILE LYS GLU GLU ASN SEQRES 11 A 564 GLU LYS LEU LEU LYS GLU TYR GLY PHE CYS ILE MET ASP SEQRES 12 A 564 ASN HIS LYS GLU ARG ILE ALA ASN PHE LYS ILE GLU PRO SEQRES 13 A 564 PRO GLY LEU PHE ARG GLY ARG GLY ASN HIS PRO LYS MET SEQRES 14 A 564 GLY MET LEU LYS ARG ARG ILE MET PRO GLU ASP ILE ILE SEQRES 15 A 564 ILE ASN CYS SER LYS ASP ALA LYS VAL PRO SER PRO PRO SEQRES 16 A 564 PRO GLY HIS LYS TRP LYS GLU VAL ARG HIS ASP ASN LYS SEQRES 17 A 564 VAL THR TRP LEU VAL SER TRP THR GLU ASN ILE GLN GLY SEQRES 18 A 564 SER ILE LYS TYR ILE MET LEU ASN PRO SER SER ARG ILE SEQRES 19 A 564 LYS GLY GLU LYS ASP TRP GLN LYS TYR GLU THR ALA ARG SEQRES 20 A 564 ARG LEU LYS LYS CYS VAL ASP LYS ILE ARG ASN GLN TYR SEQRES 21 A 564 ARG GLU ASP TRP LYS SER LYS GLU MET LYS VAL ARG GLN SEQRES 22 A 564 ARG ALA VAL ALA LEU TYR PHE ILE ASP LYS LEU ALA LEU SEQRES 23 A 564 ARG ALA GLY ASN GLU LYS GLU GLU GLY GLU THR ALA ASP SEQRES 24 A 564 THR VAL GLY CYS CYS SER LEU ARG VAL GLU HIS ILE ASN SEQRES 25 A 564 LEU HIS PRO GLU LEU ASP GLY GLN GLU TYR VAL VAL GLU SEQRES 26 A 564 PHE ASP PHE LEU GLY LYS ASP SER ILE ARG TYR TYR ASN SEQRES 27 A 564 LYS VAL PRO VAL GLU LYS ARG VAL PHE LYS ASN LEU GLN SEQRES 28 A 564 LEU PHE MET GLU ASN LYS GLN PRO GLU ASP ASP LEU PHE SEQRES 29 A 564 ASP ARG LEU ASN THR GLY ILE LEU ASN LYS HIS LEU GLN SEQRES 30 A 564 ASP LEU MET GLU GLY LEU THR ALA LYS VAL PHE ARG THR SEQRES 31 A 564 TYR ASN ALA SER ILE THR LEU GLN GLN GLN LEU LYS GLU SEQRES 32 A 564 LEU THR ALA PRO ASP GLU ASN ILE PRO ALA LYS ILE LEU SEQRES 33 A 564 SER TYR ASN ARG ALA ASN ARG ALA VAL ALA ILE LEU CYS SEQRES 34 A 564 ASN HIS GLN ARG ALA PRO PRO LYS THR PHE GLU LYS SER SEQRES 35 A 564 MET MET ASN LEU GLN THR LYS ILE ASP ALA LYS LYS GLU SEQRES 36 A 564 GLN LEU ALA ASP ALA ARG ARG ASP LEU LYS SER ALA LYS SEQRES 37 A 564 ALA ASP ALA LYS VAL MET LYS ASP ALA LYS THR LYS LYS SEQRES 38 A 564 VAL VAL GLU SER LYS LYS LYS ALA VAL GLN ARG LEU GLU SEQRES 39 A 564 GLU GLN LEU MET LYS LEU GLU VAL GLN ALA THR ASP ARG SEQRES 40 A 564 GLU GLU ASN LYS GLN ILE ALA LEU GLY THR SER LYS LEU SEQRES 41 A 564 ASN PHE LEU ASP PRO ARG ILE THR VAL ALA TRP CYS LYS SEQRES 42 A 564 LYS TRP GLY VAL PRO ILE GLU LYS ILE TYR ASN LYS THR SEQRES 43 A 564 GLN ARG GLU LYS PHE ALA TRP ALA ILE ASP MET ALA ASP SEQRES 44 A 564 GLU ASP TYR GLU PHE MODRES 1LPQ 8OG B 11 DG HET 8OG B 11 23 HETNAM 8OG 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETSYN 8OG 8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE FORMUL 1 8OG C10 H14 N5 O8 P FORMUL 4 HOH *27(H2 O) HELIX 1 1 LYS A 204 GLU A 208 5 5 HELIX 2 2 SER A 250 LYS A 262 1 13 HELIX 3 3 HIS A 266 THR A 270 5 5 HELIX 4 4 LYS A 271 GLU A 285 1 15 HELIX 5 5 THR A 287 ASN A 292 1 6 HELIX 6 6 PHE A 302 LYS A 317 1 16 HELIX 7 7 SER A 320 TYR A 338 1 19 HELIX 8 8 LYS A 436 LYS A 451 1 16 HELIX 9 9 VAL A 454 GLU A 463 1 10 HELIX 10 10 GLN A 474 LEU A 485 1 12 HELIX 11 11 ARG A 508 GLU A 510 5 3 HELIX 12 12 LYS A 532 SER A 534 5 3 HELIX 13 13 GLU A 544 PHE A 554 1 11 HELIX 14 14 ASN A 569 MET A 581 1 13 HELIX 15 15 THR A 585 THR A 606 1 22 HELIX 16 16 ASN A 611 ASN A 623 1 13 HELIX 17 17 ARG A 624 ILE A 628 5 5 HELIX 18 18 LEU A 647 ARG A 663 1 17 HELIX 19 19 LYS A 666 LYS A 673 1 8 HELIX 20 20 LYS A 679 LYS A 682 5 4 HELIX 21 21 VAL A 683 LYS A 688 1 6 HELIX 22 22 LYS A 688 LYS A 700 1 13 HELIX 23 23 LEU A 701 ARG A 708 1 8 HELIX 24 24 ASP A 725 TRP A 736 1 12 HELIX 25 25 PRO A 739 TYR A 744 1 6 HELIX 26 26 ASN A 745 PHE A 752 1 8 HELIX 27 27 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 HIS A 346 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 2 ILE A 383 ILE A 384 0 SHEET 2 D 2 GLU A 403 VAL A 404 1 O GLU A 403 N ILE A 384 SHEET 1 E 2 TRP A 416 THR A 417 0 SHEET 2 E 2 ILE A 424 LYS A 425 -1 O LYS A 425 N TRP A 416 SHEET 1 F 3 ILE A 512 GLU A 517 0 SHEET 2 F 3 GLU A 522 LEU A 530 -1 O VAL A 524 N HIS A 515 SHEET 3 F 3 ARG A 536 PRO A 542 -1 O TYR A 537 N PHE A 529 LINK O3' DT B 10 P 8OG B 11 1555 1555 1.59 LINK O3' 8OG B 11 P DG B 12 1555 1555 1.60 CRYST1 57.200 122.500 72.000 90.00 97.40 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 0.017483 0.000000 0.002271 0.00000 SCALE2 0.000000 0.008163 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014006 0.00000