HEADER HYDROLASE 18-MAY-22 8CVQ TITLE CRYSTAL STRUCTURE OF TDP1 COMPLEXED WITH COMPOUND XZ761 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYROSYL-DNA PHOSPHODIESTERASE 1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: TYR-DNA PHOSPHODIESTERASE 1; COMPND 5 EC: 3.1.4.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: TDP1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PHOSPHODIESTERASE, DNA BINDING PROTEIN, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR G.T.LOUNTOS,X.Z.ZHAO,W.WANG,E.KISELEV,J.E.TROPEA,D.NEEDLE,Y.POMMIER, AUTHOR 2 T.R.BURKE REVDAT 3 25-OCT-23 8CVQ 1 REMARK REVDAT 2 31-MAY-23 8CVQ 1 JRNL REVDAT 1 12-APR-23 8CVQ 0 JRNL AUTH X.Z.ZHAO,W.WANG,G.T.LOUNTOS,E.KISELEV,J.E.TROPEA,D.NEEDLE, JRNL AUTH 2 Y.POMMIER,T.R.BURKE JR. JRNL TITL IDENTIFICATION OF MULTIDENTATE TYROSYL-DNA PHOSPHODIESTERASE JRNL TITL 2 1 (TDP1) INHIBITORS THAT SIMULTANEOUSLY ACCESS THE DNA, JRNL TITL 3 PROTEIN AND CATALYTIC-BINDING SITES BY OXIME JRNL TITL 4 DIVERSIFICATION. JRNL REF RSC CHEM BIOL V. 4 334 2023 JRNL REFN ESSN 2633-0679 JRNL PMID 37181631 JRNL DOI 10.1039/D2CB00230B REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.12 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 122293 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 6086 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 46.1000 - 5.1254 1.00 4220 201 0.1837 0.1963 REMARK 3 2 5.1254 - 4.0690 1.00 4018 195 0.1435 0.1535 REMARK 3 3 4.0690 - 3.5548 1.00 3936 223 0.1540 0.1880 REMARK 3 4 3.5548 - 3.2299 1.00 3982 190 0.1596 0.1732 REMARK 3 5 3.2299 - 2.9985 1.00 3899 221 0.1690 0.1880 REMARK 3 6 2.9985 - 2.8217 1.00 3891 215 0.1722 0.2037 REMARK 3 7 2.8217 - 2.6804 1.00 3892 209 0.1646 0.1952 REMARK 3 8 2.6804 - 2.5637 1.00 3900 217 0.1646 0.1862 REMARK 3 9 2.5637 - 2.4650 1.00 3877 194 0.1676 0.1801 REMARK 3 10 2.4650 - 2.3800 1.00 3877 186 0.1605 0.1891 REMARK 3 11 2.3800 - 2.3056 1.00 3926 189 0.1598 0.1919 REMARK 3 12 2.3056 - 2.2397 1.00 3838 217 0.1691 0.1853 REMARK 3 13 2.2397 - 2.1807 1.00 3850 213 0.1573 0.2036 REMARK 3 14 2.1807 - 2.1275 1.00 3864 191 0.1534 0.1855 REMARK 3 15 2.1275 - 2.0791 1.00 3865 178 0.1579 0.2052 REMARK 3 16 2.0791 - 2.0349 1.00 3879 202 0.1572 0.2042 REMARK 3 17 2.0349 - 1.9942 1.00 3850 181 0.1521 0.1712 REMARK 3 18 1.9942 - 1.9566 1.00 3854 227 0.1706 0.2031 REMARK 3 19 1.9566 - 1.9216 1.00 3806 208 0.1735 0.2302 REMARK 3 20 1.9216 - 1.8890 1.00 3885 195 0.1805 0.2216 REMARK 3 21 1.8890 - 1.8586 1.00 3855 196 0.1656 0.1942 REMARK 3 22 1.8586 - 1.8300 1.00 3824 201 0.1667 0.1963 REMARK 3 23 1.8300 - 1.8031 1.00 3860 203 0.1796 0.2394 REMARK 3 24 1.8031 - 1.7777 1.00 3762 204 0.1792 0.2174 REMARK 3 25 1.7777 - 1.7536 1.00 3872 225 0.1858 0.2284 REMARK 3 26 1.7536 - 1.7309 1.00 3812 188 0.1907 0.2559 REMARK 3 27 1.7309 - 1.7092 1.00 3822 210 0.2039 0.2230 REMARK 3 28 1.7092 - 1.6886 1.00 3842 214 0.2192 0.2542 REMARK 3 29 1.6886 - 1.6690 1.00 3817 199 0.2294 0.2684 REMARK 3 30 1.6690 - 1.6502 0.94 3632 194 0.2414 0.2660 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.490 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.79 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 162 THROUGH 285 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.5893 0.5143 -35.5156 REMARK 3 T TENSOR REMARK 3 T11: 0.1107 T22: 0.0916 REMARK 3 T33: 0.1132 T12: 0.0242 REMARK 3 T13: -0.0025 T23: -0.0093 REMARK 3 L TENSOR REMARK 3 L11: 1.3827 L22: 0.7849 REMARK 3 L33: 1.2287 L12: -0.1865 REMARK 3 L13: 0.1793 L23: -0.1983 REMARK 3 S TENSOR REMARK 3 S11: -0.0557 S12: -0.1723 S13: 0.0906 REMARK 3 S21: 0.0617 S22: 0.0350 S23: 0.0838 REMARK 3 S31: -0.0663 S32: -0.1159 S33: 0.0162 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 286 THROUGH 452 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.9386 -9.7912 -49.3214 REMARK 3 T TENSOR REMARK 3 T11: 0.0931 T22: 0.0480 REMARK 3 T33: 0.1135 T12: -0.0191 REMARK 3 T13: 0.0001 T23: -0.0035 REMARK 3 L TENSOR REMARK 3 L11: 1.1105 L22: 0.5536 REMARK 3 L33: 1.2732 L12: -0.2410 REMARK 3 L13: 0.3099 L23: -0.1656 REMARK 3 S TENSOR REMARK 3 S11: 0.0255 S12: 0.0940 S13: -0.0701 REMARK 3 S21: -0.0713 S22: -0.0282 S23: 0.0177 REMARK 3 S31: 0.1167 S32: 0.0114 S33: 0.0170 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 453 THROUGH 607 ) REMARK 3 ORIGIN FOR THE GROUP (A): 19.3144 -13.1675 -38.6389 REMARK 3 T TENSOR REMARK 3 T11: 0.1062 T22: 0.0709 REMARK 3 T33: 0.1345 T12: 0.0109 REMARK 3 T13: -0.0034 T23: 0.0102 REMARK 3 L TENSOR REMARK 3 L11: 1.0382 L22: 0.2685 REMARK 3 L33: 1.1821 L12: 0.0938 REMARK 3 L13: 0.2842 L23: 0.0817 REMARK 3 S TENSOR REMARK 3 S11: 0.0306 S12: -0.0506 S13: -0.0363 REMARK 3 S21: 0.0357 S22: -0.0278 S23: -0.0103 REMARK 3 S31: 0.1266 S32: 0.1110 S33: 0.0066 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 162 THROUGH 359 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.5437 8.6178 -84.5683 REMARK 3 T TENSOR REMARK 3 T11: 0.1168 T22: 0.2272 REMARK 3 T33: 0.1563 T12: -0.0437 REMARK 3 T13: -0.0001 T23: 0.0780 REMARK 3 L TENSOR REMARK 3 L11: 1.2902 L22: 0.7524 REMARK 3 L33: 2.4794 L12: -0.1517 REMARK 3 L13: 0.5080 L23: -0.1993 REMARK 3 S TENSOR REMARK 3 S11: -0.0390 S12: 0.2414 S13: 0.1334 REMARK 3 S21: -0.0474 S22: -0.1058 S23: -0.1453 REMARK 3 S31: -0.1886 S32: 0.4953 S33: 0.0613 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 360 THROUGH 452 ) REMARK 3 ORIGIN FOR THE GROUP (A): -2.0169 -11.0985 -84.4772 REMARK 3 T TENSOR REMARK 3 T11: 0.2492 T22: 0.1833 REMARK 3 T33: 0.1767 T12: -0.0438 REMARK 3 T13: 0.0135 T23: 0.0251 REMARK 3 L TENSOR REMARK 3 L11: 0.9820 L22: 0.6922 REMARK 3 L33: 2.0702 L12: 0.0287 REMARK 3 L13: 0.1718 L23: -0.0948 REMARK 3 S TENSOR REMARK 3 S11: 0.0342 S12: -0.1067 S13: -0.2268 REMARK 3 S21: 0.0031 S22: 0.0096 S23: 0.0190 REMARK 3 S31: 0.6578 S32: -0.2707 S33: -0.0206 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 453 THROUGH 607 ) REMARK 3 ORIGIN FOR THE GROUP (A): -4.0822 -3.0306 -91.9405 REMARK 3 T TENSOR REMARK 3 T11: 0.1154 T22: 0.1695 REMARK 3 T33: 0.1280 T12: -0.0117 REMARK 3 T13: 0.0103 T23: 0.0082 REMARK 3 L TENSOR REMARK 3 L11: 0.7337 L22: 0.3102 REMARK 3 L33: 2.5428 L12: 0.1113 REMARK 3 L13: 0.4025 L23: -0.2879 REMARK 3 S TENSOR REMARK 3 S11: 0.0191 S12: 0.0684 S13: -0.0455 REMARK 3 S21: -0.0507 S22: -0.0133 S23: 0.0072 REMARK 3 S31: 0.2346 S32: -0.2694 S33: -0.0146 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8CVQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-MAY-22. REMARK 100 THE DEPOSITION ID IS D_1000265406. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-DEC-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 122293 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.72400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 6DHU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MOPS/HEPES-NA PH 7.5, 10% (W/V) REMARK 280 PEG 8000, 20% (V/V) ETHYLENE GLYCOL, 0.03 M SODIUM FLUORIDE, REMARK 280 0.03 M SODIUM BROMIDE AND 0.03 M SODIUM IODIDE, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 24.89750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 96.44850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 52.50600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 96.44850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.89750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 52.50600 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 SER A 148 REMARK 465 GLY A 149 REMARK 465 GLU A 150 REMARK 465 GLY A 151 REMARK 465 GLN A 152 REMARK 465 ASP A 153 REMARK 465 ILE A 154 REMARK 465 TRP A 155 REMARK 465 ASP A 156 REMARK 465 MET A 157 REMARK 465 LEU A 158 REMARK 465 ASP A 159 REMARK 465 LYS A 160 REMARK 465 GLY A 161 REMARK 465 LYS A 428 REMARK 465 THR A 429 REMARK 465 PRO A 430 REMARK 465 GLY A 431 REMARK 465 LYS A 432 REMARK 465 GLY A 562 REMARK 465 SER A 563 REMARK 465 GLN A 564 REMARK 465 GLU A 565 REMARK 465 SER A 608 REMARK 465 SER B 148 REMARK 465 GLY B 149 REMARK 465 GLU B 150 REMARK 465 GLY B 151 REMARK 465 GLN B 152 REMARK 465 ASP B 153 REMARK 465 ILE B 154 REMARK 465 TRP B 155 REMARK 465 ASP B 156 REMARK 465 MET B 157 REMARK 465 LEU B 158 REMARK 465 ASP B 159 REMARK 465 LYS B 160 REMARK 465 GLY B 161 REMARK 465 LYS B 428 REMARK 465 THR B 429 REMARK 465 PRO B 430 REMARK 465 GLY B 431 REMARK 465 LYS B 432 REMARK 465 GLY B 562 REMARK 465 SER B 563 REMARK 465 GLN B 564 REMARK 465 GLU B 565 REMARK 465 SER B 608 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 B 246 CG CD OE1 OE2 REMARK 470 MET B 567 CG SD CE 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 ARG A 232 -130.08 53.99 REMARK 500 HIS A 290 -66.68 -94.14 REMARK 500 TRP A 411 -47.96 -156.21 REMARK 500 SER A 414 -71.06 -106.55 REMARK 500 GLN A 470 49.03 -144.21 REMARK 500 ALA A 482 47.00 -145.30 REMARK 500 ARG B 232 -127.17 51.38 REMARK 500 HIS B 290 -65.99 -99.32 REMARK 500 TRP B 411 -45.93 -160.62 REMARK 500 SER B 414 -66.46 -92.75 REMARK 500 GLN B 470 48.45 -151.72 REMARK 500 ALA B 482 47.08 -145.90 REMARK 500 REMARK 500 REMARK: NULL DBREF 8CVQ A 148 608 UNP Q9NUW8 TYDP1_HUMAN 148 608 DBREF 8CVQ B 148 608 UNP Q9NUW8 TYDP1_HUMAN 148 608 SEQRES 1 A 461 SER GLY GLU GLY GLN ASP ILE TRP ASP MET LEU ASP LYS SEQRES 2 A 461 GLY ASN PRO PHE GLN PHE TYR LEU THR ARG VAL SER GLY SEQRES 3 A 461 VAL LYS PRO LYS TYR ASN SER GLY ALA LEU HIS ILE LYS SEQRES 4 A 461 ASP ILE LEU SER PRO LEU PHE GLY THR LEU VAL SER SER SEQRES 5 A 461 ALA GLN PHE ASN TYR CYS PHE ASP VAL ASP TRP LEU VAL SEQRES 6 A 461 LYS GLN TYR PRO PRO GLU PHE ARG LYS LYS PRO ILE LEU SEQRES 7 A 461 LEU VAL HIS GLY ASP LYS ARG GLU ALA LYS ALA HIS LEU SEQRES 8 A 461 HIS ALA GLN ALA LYS PRO TYR GLU ASN ILE SER LEU CYS SEQRES 9 A 461 GLN ALA LYS LEU ASP ILE ALA PHE GLY THR HIS HIS THR SEQRES 10 A 461 LYS MET MET LEU LEU LEU TYR GLU GLU GLY LEU ARG VAL SEQRES 11 A 461 VAL ILE HIS THR SER ASN LEU ILE HIS ALA ASP TRP HIS SEQRES 12 A 461 GLN LYS THR GLN GLY ILE TRP LEU SER PRO LEU TYR PRO SEQRES 13 A 461 ARG ILE ALA ASP GLY THR HIS LYS SER GLY GLU SER PRO SEQRES 14 A 461 THR HIS PHE LYS ALA ASP LEU ILE SER TYR LEU MET ALA SEQRES 15 A 461 TYR ASN ALA PRO SER LEU LYS GLU TRP ILE ASP VAL ILE SEQRES 16 A 461 HIS LYS HIS ASP LEU SER GLU THR ASN VAL TYR LEU ILE SEQRES 17 A 461 GLY SER THR PRO GLY ARG PHE GLN GLY SER GLN LYS ASP SEQRES 18 A 461 ASN TRP GLY HIS PHE ARG LEU LYS LYS LEU LEU LYS ASP SEQRES 19 A 461 HIS ALA SER SER MET PRO ASN ALA GLU SER TRP PRO VAL SEQRES 20 A 461 VAL GLY GLN PHE SER SER VAL GLY SER LEU GLY ALA ASP SEQRES 21 A 461 GLU SER LYS TRP LEU CYS SER GLU PHE LYS GLU SER MET SEQRES 22 A 461 LEU THR LEU GLY LYS GLU SER LYS THR PRO GLY LYS SER SEQRES 23 A 461 SER VAL PRO LEU TYR LEU ILE TYR PRO SER VAL GLU ASN SEQRES 24 A 461 VAL ARG THR SER LEU GLU GLY TYR PRO ALA GLY GLY SER SEQRES 25 A 461 LEU PRO TYR SER ILE GLN THR ALA GLU LYS GLN ASN TRP SEQRES 26 A 461 LEU HIS SER TYR PHE HIS LYS TRP SER ALA GLU THR SER SEQRES 27 A 461 GLY ARG SER ASN ALA MET PRO HIS ILE LYS THR TYR MET SEQRES 28 A 461 ARG PRO SER PRO ASP PHE SER LYS ILE ALA TRP PHE LEU SEQRES 29 A 461 VAL THR SER ALA ASN LEU SER LYS ALA ALA TRP GLY ALA SEQRES 30 A 461 LEU GLU LYS ASN GLY THR GLN LEU MET ILE ARG SER TYR SEQRES 31 A 461 GLU LEU GLY VAL LEU PHE LEU PRO SER ALA PHE GLY LEU SEQRES 32 A 461 ASP SER PHE LYS VAL LYS GLN LYS PHE PHE ALA GLY SER SEQRES 33 A 461 GLN GLU PRO MET ALA THR PHE PRO VAL PRO TYR ASP LEU SEQRES 34 A 461 PRO PRO GLU LEU TYR GLY SER LYS ASP ARG PRO TRP ILE SEQRES 35 A 461 TRP ASN ILE PRO TYR VAL LYS ALA PRO ASP THR HIS GLY SEQRES 36 A 461 ASN MET TRP VAL PRO SER SEQRES 1 B 461 SER GLY GLU GLY GLN ASP ILE TRP ASP MET LEU ASP LYS SEQRES 2 B 461 GLY ASN PRO PHE GLN PHE TYR LEU THR ARG VAL SER GLY SEQRES 3 B 461 VAL LYS PRO LYS TYR ASN SER GLY ALA LEU HIS ILE LYS SEQRES 4 B 461 ASP ILE LEU SER PRO LEU PHE GLY THR LEU VAL SER SER SEQRES 5 B 461 ALA GLN PHE ASN TYR CYS PHE ASP VAL ASP TRP LEU VAL SEQRES 6 B 461 LYS GLN TYR PRO PRO GLU PHE ARG LYS LYS PRO ILE LEU SEQRES 7 B 461 LEU VAL HIS GLY ASP LYS ARG GLU ALA LYS ALA HIS LEU SEQRES 8 B 461 HIS ALA GLN ALA LYS PRO TYR GLU ASN ILE SER LEU CYS SEQRES 9 B 461 GLN ALA LYS LEU ASP ILE ALA PHE GLY THR HIS HIS THR SEQRES 10 B 461 LYS MET MET LEU LEU LEU TYR GLU GLU GLY LEU ARG VAL SEQRES 11 B 461 VAL ILE HIS THR SER ASN LEU ILE HIS ALA ASP TRP HIS SEQRES 12 B 461 GLN LYS THR GLN GLY ILE TRP LEU SER PRO LEU TYR PRO SEQRES 13 B 461 ARG ILE ALA ASP GLY THR HIS LYS SER GLY GLU SER PRO SEQRES 14 B 461 THR HIS PHE LYS ALA ASP LEU ILE SER TYR LEU MET ALA SEQRES 15 B 461 TYR ASN ALA PRO SER LEU LYS GLU TRP ILE ASP VAL ILE SEQRES 16 B 461 HIS LYS HIS ASP LEU SER GLU THR ASN VAL TYR LEU ILE SEQRES 17 B 461 GLY SER THR PRO GLY ARG PHE GLN GLY SER GLN LYS ASP SEQRES 18 B 461 ASN TRP GLY HIS PHE ARG LEU LYS LYS LEU LEU LYS ASP SEQRES 19 B 461 HIS ALA SER SER MET PRO ASN ALA GLU SER TRP PRO VAL SEQRES 20 B 461 VAL GLY GLN PHE SER SER VAL GLY SER LEU GLY ALA ASP SEQRES 21 B 461 GLU SER LYS TRP LEU CYS SER GLU PHE LYS GLU SER MET SEQRES 22 B 461 LEU THR LEU GLY LYS GLU SER LYS THR PRO GLY LYS SER SEQRES 23 B 461 SER VAL PRO LEU TYR LEU ILE TYR PRO SER VAL GLU ASN SEQRES 24 B 461 VAL ARG THR SER LEU GLU GLY TYR PRO ALA GLY GLY SER SEQRES 25 B 461 LEU PRO TYR SER ILE GLN THR ALA GLU LYS GLN ASN TRP SEQRES 26 B 461 LEU HIS SER TYR PHE HIS LYS TRP SER ALA GLU THR SER SEQRES 27 B 461 GLY ARG SER ASN ALA MET PRO HIS ILE LYS THR TYR MET SEQRES 28 B 461 ARG PRO SER PRO ASP PHE SER LYS ILE ALA TRP PHE LEU SEQRES 29 B 461 VAL THR SER ALA ASN LEU SER LYS ALA ALA TRP GLY ALA SEQRES 30 B 461 LEU GLU LYS ASN GLY THR GLN LEU MET ILE ARG SER TYR SEQRES 31 B 461 GLU LEU GLY VAL LEU PHE LEU PRO SER ALA PHE GLY LEU SEQRES 32 B 461 ASP SER PHE LYS VAL LYS GLN LYS PHE PHE ALA GLY SER SEQRES 33 B 461 GLN GLU PRO MET ALA THR PHE PRO VAL PRO TYR ASP LEU SEQRES 34 B 461 PRO PRO GLU LEU TYR GLY SER LYS ASP ARG PRO TRP ILE SEQRES 35 B 461 TRP ASN ILE PRO TYR VAL LYS ALA PRO ASP THR HIS GLY SEQRES 36 B 461 ASN MET TRP VAL PRO SER HET OYH A 701 34 HET MPO A 702 13 HET EDO A 703 4 HET EDO A 704 4 HET EDO A 705 4 HET OYH B 701 34 HET MPO B 702 13 HET EDO B 703 4 HET EDO B 704 4 HET EDO B 705 4 HET EDO B 706 4 HETNAM OYH 4-{[(4S)-2,7-DIPHENYLIMIDAZO[1,2-A]PYRIDIN-3- HETNAM 2 OYH YL]AMINO}BENZENE-1,2-DICARBOXYLIC ACID HETNAM MPO 3[N-MORPHOLINO]PROPANE SULFONIC ACID HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 OYH 2(C27 H19 N3 O4) FORMUL 4 MPO 2(C7 H15 N O4 S) FORMUL 5 EDO 7(C2 H6 O2) FORMUL 14 HOH *793(H2 O) HELIX 1 AA1 LYS A 175 ASN A 179 5 5 HELIX 2 AA2 HIS A 184 LEU A 189 1 6 HELIX 3 AA3 SER A 190 GLY A 194 5 5 HELIX 4 AA4 ASP A 207 TYR A 215 1 9 HELIX 5 AA5 PRO A 216 ARG A 220 5 5 HELIX 6 AA6 LYS A 231 LYS A 243 1 13 HELIX 7 AA7 ILE A 285 HIS A 290 5 6 HELIX 8 AA8 HIS A 318 ALA A 329 1 12 HELIX 9 AA9 ALA A 332 LYS A 344 1 13 HELIX 10 AB1 SER A 365 ASN A 369 5 5 HELIX 11 AB2 TRP A 370 ALA A 383 1 14 HELIX 12 AB3 ASN A 388 TRP A 392 5 5 HELIX 13 AB4 SER A 414 THR A 422 1 9 HELIX 14 AB5 SER A 443 THR A 449 1 7 HELIX 15 AB6 GLY A 453 LEU A 460 5 8 HELIX 16 AB7 SER A 463 GLU A 468 1 6 HELIX 17 AB8 LYS A 469 SER A 475 5 7 HELIX 18 AB9 ALA A 482 GLY A 486 5 5 HELIX 19 AC1 SER A 518 GLY A 523 1 6 HELIX 20 AC2 LEU A 544 GLY A 549 5 6 HELIX 21 AC3 LYS B 175 ASN B 179 5 5 HELIX 22 AC4 HIS B 184 LEU B 189 1 6 HELIX 23 AC5 SER B 190 GLY B 194 5 5 HELIX 24 AC6 ASP B 207 TYR B 215 1 9 HELIX 25 AC7 PRO B 216 ARG B 220 5 5 HELIX 26 AC8 LYS B 231 LYS B 243 1 13 HELIX 27 AC9 ILE B 285 HIS B 290 5 6 HELIX 28 AD1 HIS B 318 ALA B 329 1 12 HELIX 29 AD2 ALA B 332 LYS B 344 1 13 HELIX 30 AD3 SER B 365 ASN B 369 5 5 HELIX 31 AD4 TRP B 370 ALA B 383 1 14 HELIX 32 AD5 ASN B 388 TRP B 392 5 5 HELIX 33 AD6 GLU B 415 THR B 422 1 8 HELIX 34 AD7 SER B 443 THR B 449 1 7 HELIX 35 AD8 GLY B 453 LEU B 460 5 8 HELIX 36 AD9 SER B 463 GLU B 468 1 6 HELIX 37 AE1 LYS B 469 SER B 475 5 7 HELIX 38 AE2 ALA B 482 GLY B 486 5 5 HELIX 39 AE3 SER B 518 GLY B 523 1 6 HELIX 40 AE4 LEU B 544 GLY B 549 5 6 SHEET 1 AA1 7 PHE A 166 LEU A 168 0 SHEET 2 AA1 7 GLY A 295 LEU A 298 -1 O ILE A 296 N TYR A 167 SHEET 3 AA1 7 LEU A 275 HIS A 280 -1 N ILE A 279 O TRP A 297 SHEET 4 AA1 7 MET A 266 TYR A 271 -1 N MET A 267 O VAL A 278 SHEET 5 AA1 7 LEU A 196 PHE A 202 -1 N VAL A 197 O LEU A 270 SHEET 6 AA1 7 ILE A 224 HIS A 228 1 O LEU A 225 N GLN A 201 SHEET 7 AA1 7 ILE A 248 GLN A 252 1 O CYS A 251 N LEU A 226 SHEET 1 AA2 7 TYR A 353 SER A 357 0 SHEET 2 AA2 7 GLU A 538 PHE A 543 -1 O LEU A 542 N TYR A 353 SHEET 3 AA2 7 LYS A 506 THR A 513 -1 N PHE A 510 O PHE A 543 SHEET 4 AA2 7 LYS A 495 PRO A 500 -1 N ARG A 499 O ALA A 508 SHEET 5 AA2 7 VAL A 394 GLN A 397 -1 N VAL A 395 O MET A 498 SHEET 6 AA2 7 LEU A 437 ILE A 440 1 O ILE A 440 N GLY A 396 SHEET 7 AA2 7 PHE A 477 HIS A 478 1 O HIS A 478 N LEU A 439 SHEET 1 AA3 5 TYR A 353 SER A 357 0 SHEET 2 AA3 5 GLU A 538 PHE A 543 -1 O LEU A 542 N TYR A 353 SHEET 3 AA3 5 LYS A 506 THR A 513 -1 N PHE A 510 O PHE A 543 SHEET 4 AA3 5 PHE A 553 VAL A 555 -1 O PHE A 553 N ILE A 507 SHEET 5 AA3 5 THR A 569 PHE A 570 1 O PHE A 570 N LYS A 554 SHEET 1 AA4 3 GLY A 360 GLN A 363 0 SHEET 2 AA4 3 GLN A 531 ILE A 534 -1 O LEU A 532 N PHE A 362 SHEET 3 AA4 3 ALA A 524 GLU A 526 -1 N GLU A 526 O GLN A 531 SHEET 1 AA5 7 PHE B 166 LEU B 168 0 SHEET 2 AA5 7 GLY B 295 LEU B 298 -1 O ILE B 296 N TYR B 167 SHEET 3 AA5 7 LEU B 275 HIS B 280 -1 N ILE B 279 O TRP B 297 SHEET 4 AA5 7 MET B 266 TYR B 271 -1 N MET B 267 O VAL B 278 SHEET 5 AA5 7 LEU B 196 PHE B 202 -1 N VAL B 197 O LEU B 270 SHEET 6 AA5 7 ILE B 224 HIS B 228 1 O LEU B 225 N GLN B 201 SHEET 7 AA5 7 ILE B 248 GLN B 252 1 O SER B 249 N ILE B 224 SHEET 1 AA6 7 TYR B 353 SER B 357 0 SHEET 2 AA6 7 GLU B 538 PHE B 543 -1 O LEU B 542 N TYR B 353 SHEET 3 AA6 7 LYS B 506 THR B 513 -1 N PHE B 510 O PHE B 543 SHEET 4 AA6 7 LYS B 495 PRO B 500 -1 N ARG B 499 O ALA B 508 SHEET 5 AA6 7 VAL B 394 GLN B 397 -1 N VAL B 395 O MET B 498 SHEET 6 AA6 7 LEU B 437 ILE B 440 1 O ILE B 440 N GLY B 396 SHEET 7 AA6 7 PHE B 477 HIS B 478 1 O HIS B 478 N LEU B 439 SHEET 1 AA7 5 TYR B 353 SER B 357 0 SHEET 2 AA7 5 GLU B 538 PHE B 543 -1 O LEU B 542 N TYR B 353 SHEET 3 AA7 5 LYS B 506 THR B 513 -1 N PHE B 510 O PHE B 543 SHEET 4 AA7 5 PHE B 553 VAL B 555 -1 O PHE B 553 N ILE B 507 SHEET 5 AA7 5 THR B 569 PHE B 570 1 O PHE B 570 N LYS B 554 SHEET 1 AA8 3 GLY B 360 GLN B 363 0 SHEET 2 AA8 3 GLN B 531 ILE B 534 -1 O LEU B 532 N PHE B 362 SHEET 3 AA8 3 ALA B 524 GLU B 526 -1 N GLU B 526 O GLN B 531 CISPEP 1 LEU A 576 PRO A 577 0 -7.05 CISPEP 2 ASN B 162 PRO B 163 0 2.83 CISPEP 3 LEU B 576 PRO B 577 0 -5.16 CRYST1 49.795 105.012 192.897 90.00 90.00 90.00 P 21 21 21 8 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 0.020082 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009523 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005184 0.00000