HEADER HYDROLASE/HYDROLASE INHIBITOR 19-MAR-20 6W7L TITLE STRUCTURE OF TDP1 CATALYTIC DOMAIN IN COMPLEX WITH INHIBITOR XZ632P 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, INHIBITOR, CANCER DRUG TARGET, DNA BINDING KEYWDS 2 PROTEIN, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR G.T.LOUNTOS,X.Z.ZHAO,E.KISELEV,J.E.TROPEA,D.NEEDLE,Y.POMMIER, AUTHOR 2 T.R.BURKE,D.S.WAUGH REVDAT 3 18-OCT-23 6W7L 1 REMARK REVDAT 2 31-MAR-21 6W7L 1 JRNL REVDAT 1 24-MAR-21 6W7L 0 JRNL AUTH X.Z.ZHAO,E.KISELEV,G.T.LOUNTOS,W.WANG,J.E.TROPEA,D.NEEDLE, JRNL AUTH 2 T.A.HILIMIRE,J.S.SCHNEEKLOTH,D.S.WAUGH,Y.POMMIER,T.R.BURKE JRNL TITL SMALL MOLECULE MICROARRAY IDENTIFIES INHIBITORS OF JRNL TITL 2 TYROSYL-DNA PHOSPHODIESTERASE 1 THAT SIMULTANEOUSLY ACCESS JRNL TITL 3 THE CATALYTIC POCKET AND TWO SUBSTRATE BINDING SITES JRNL REF CHEMICAL SCIENCE V. 12 3876 2021 JRNL DOI 10.1039/D0SC05411A REMARK 2 REMARK 2 RESOLUTION. 1.86 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.86 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.55 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 87278 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 4279 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 48.5530 - 5.7650 0.98 3007 151 0.2013 0.2237 REMARK 3 2 5.7650 - 4.5770 0.98 2815 151 0.1560 0.1775 REMARK 3 3 4.5770 - 3.9987 0.97 2810 147 0.1420 0.1692 REMARK 3 4 3.9987 - 3.6332 0.99 2797 147 0.1534 0.1879 REMARK 3 5 3.6332 - 3.3729 0.99 2795 151 0.1682 0.2059 REMARK 3 6 3.3729 - 3.1741 1.00 2823 129 0.1758 0.1820 REMARK 3 7 3.1741 - 3.0151 1.00 2806 156 0.1869 0.2289 REMARK 3 8 3.0151 - 2.8839 1.00 2800 154 0.1919 0.2456 REMARK 3 9 2.8839 - 2.7729 1.00 2790 129 0.1884 0.2336 REMARK 3 10 2.7729 - 2.6772 1.00 2815 144 0.1857 0.2381 REMARK 3 11 2.6772 - 2.5935 1.00 2747 161 0.1918 0.2797 REMARK 3 12 2.5935 - 2.5194 0.99 2746 126 0.2007 0.2581 REMARK 3 13 2.5194 - 2.4531 0.99 2778 151 0.1969 0.2466 REMARK 3 14 2.4531 - 2.3932 1.00 2767 127 0.1945 0.2389 REMARK 3 15 2.3932 - 2.3388 1.00 2774 160 0.1954 0.2236 REMARK 3 16 2.3388 - 2.2890 1.00 2766 123 0.1867 0.2184 REMARK 3 17 2.2890 - 2.2433 1.00 2773 147 0.1927 0.2661 REMARK 3 18 2.2433 - 2.2009 1.00 2774 137 0.1965 0.2461 REMARK 3 19 2.2009 - 2.1616 1.00 2759 142 0.1860 0.2373 REMARK 3 20 2.1616 - 2.1250 1.00 2793 151 0.2003 0.2476 REMARK 3 21 2.1250 - 2.0907 1.00 2716 135 0.1987 0.2542 REMARK 3 22 2.0907 - 2.0585 1.00 2790 159 0.2097 0.2387 REMARK 3 23 2.0585 - 2.0283 1.00 2749 145 0.2188 0.2566 REMARK 3 24 2.0283 - 1.9997 1.00 2744 129 0.2174 0.2764 REMARK 3 25 1.9997 - 1.9727 1.00 2801 145 0.2223 0.2692 REMARK 3 26 1.9727 - 1.9470 1.00 2745 148 0.2176 0.2524 REMARK 3 27 1.9470 - 1.9227 1.00 2682 148 0.2325 0.3028 REMARK 3 28 1.9227 - 1.8995 1.00 2833 141 0.2509 0.2968 REMARK 3 29 1.8995 - 1.8774 1.00 2748 140 0.2368 0.2268 REMARK 3 30 1.8774 - 1.8564 0.83 2256 105 0.2552 0.3239 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.020 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.51 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 : NULL 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 6W7L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1000247629. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-AUG-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 87892 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.856 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.09600 REMARK 200 R SYM (I) : 0.09900 REMARK 200 FOR THE DATA SET : 38.3500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.86 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.89 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.58600 REMARK 200 R SYM FOR SHELL (I) : 0.75000 REMARK 200 FOR SHELL : 4.200 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 (%): 50.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MOPS/HEPES-NA PH 7.5 10% W/V PEG REMARK 280 8000 20% V/V ETHYLENE GLYCOL 0.03M SODIUM FLUORIDE 0.03M SODIUM REMARK 280 BROMIDE 0.03M SODIUM IODIDE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 292K 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 25.01600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 97.10550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 52.90850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 97.10550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.01600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 52.90850 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 ALA B 561 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 A 246 CG CD OE1 OE2 REMARK 470 LYS B 213 CG CD CE NZ 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: 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 HOH A 1073 O HOH A 1080 2.16 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 SER A 198 147.15 -171.83 REMARK 500 ARG A 232 -125.98 50.41 REMARK 500 HIS A 290 -69.29 -97.13 REMARK 500 TRP A 411 -47.44 -155.90 REMARK 500 GLN A 470 47.29 -147.70 REMARK 500 ALA A 482 46.63 -147.82 REMARK 500 ARG B 232 -125.72 58.80 REMARK 500 HIS B 290 -67.95 -103.78 REMARK 500 TRP B 411 -45.95 -162.13 REMARK 500 GLU B 426 -171.32 -50.39 REMARK 500 GLN B 470 47.14 -152.68 REMARK 500 ALA B 482 46.80 -148.09 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 997 DISTANCE = 6.33 ANGSTROMS REMARK 525 HOH B 998 DISTANCE = 7.30 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TGV A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TGV B 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 704 DBREF 6W7L A 148 608 UNP Q9NUW8 TYDP1_HUMAN 148 608 DBREF 6W7L 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 TGV A 701 28 HET EDO A 702 4 HET TGV B 701 28 HET EDO B 702 4 HET EDO B 703 4 HET EDO B 704 4 HETNAM TGV 4-[(2-PHENYLIMIDAZO[1,2-A]PYRAZIN-3-YL)AMINO]BENZENE-1, HETNAM 2 TGV 2-DICARBOXYLIC ACID HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 TGV 2(C20 H14 N4 O4) FORMUL 4 EDO 4(C2 H6 O2) FORMUL 9 HOH *537(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 ASP A 407 TRP A 411 5 5 HELIX 14 AB5 GLU A 415 THR A 422 1 8 HELIX 15 AB6 SER A 443 THR A 449 1 7 HELIX 16 AB7 GLY A 453 LEU A 460 5 8 HELIX 17 AB8 SER A 463 GLU A 468 1 6 HELIX 18 AB9 LYS A 469 SER A 475 5 7 HELIX 19 AC1 ALA A 482 GLY A 486 5 5 HELIX 20 AC2 SER A 518 GLY A 523 1 6 HELIX 21 AC3 LEU A 544 GLY A 549 5 6 HELIX 22 AC4 LYS B 175 SER B 180 5 6 HELIX 23 AC5 HIS B 184 LEU B 189 1 6 HELIX 24 AC6 SER B 190 GLY B 194 5 5 HELIX 25 AC7 ASP B 207 TYR B 215 1 9 HELIX 26 AC8 PRO B 216 ARG B 220 5 5 HELIX 27 AC9 LYS B 231 LYS B 243 1 13 HELIX 28 AD1 ILE B 285 HIS B 290 5 6 HELIX 29 AD2 HIS B 318 ALA B 329 1 12 HELIX 30 AD3 ALA B 332 LYS B 344 1 13 HELIX 31 AD4 SER B 365 ASN B 369 5 5 HELIX 32 AD5 TRP B 370 ALA B 383 1 14 HELIX 33 AD6 ASN B 388 TRP B 392 5 5 HELIX 34 AD7 ASP B 407 TRP B 411 5 5 HELIX 35 AD8 GLU B 415 THR B 422 1 8 HELIX 36 AD9 SER B 443 THR B 449 1 7 HELIX 37 AE1 GLY B 453 LEU B 460 5 8 HELIX 38 AE2 SER B 463 GLU B 468 1 6 HELIX 39 AE3 LYS B 469 SER B 475 5 7 HELIX 40 AE4 ALA B 482 GLY B 486 5 5 HELIX 41 AE5 SER B 518 GLY B 523 1 6 HELIX 42 AE6 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 SER A 249 N ILE A 224 SHEET 1 AA2 2 LYS A 292 THR A 293 0 SHEET 2 AA2 2 MET A 491 PRO A 492 1 O MET A 491 N THR A 293 SHEET 1 AA3 7 TYR A 353 SER A 357 0 SHEET 2 AA3 7 GLU A 538 PHE A 543 -1 O LEU A 542 N TYR A 353 SHEET 3 AA3 7 LYS A 506 THR A 513 -1 N PHE A 510 O PHE A 543 SHEET 4 AA3 7 LYS A 495 PRO A 500 -1 N ARG A 499 O ALA A 508 SHEET 5 AA3 7 VAL A 394 GLN A 397 -1 N GLN A 397 O THR A 496 SHEET 6 AA3 7 LEU A 437 ILE A 440 1 O TYR A 438 N VAL A 394 SHEET 7 AA3 7 PHE A 477 HIS A 478 1 O HIS A 478 N LEU A 439 SHEET 1 AA4 5 TYR A 353 SER A 357 0 SHEET 2 AA4 5 GLU A 538 PHE A 543 -1 O LEU A 542 N TYR A 353 SHEET 3 AA4 5 LYS A 506 THR A 513 -1 N PHE A 510 O PHE A 543 SHEET 4 AA4 5 PHE A 553 VAL A 555 -1 O PHE A 553 N ILE A 507 SHEET 5 AA4 5 THR A 569 PHE A 570 1 O PHE A 570 N LYS A 554 SHEET 1 AA5 3 GLY A 360 GLN A 363 0 SHEET 2 AA5 3 GLN A 531 ILE A 534 -1 O LEU A 532 N PHE A 362 SHEET 3 AA5 3 ALA A 524 GLU A 526 -1 N GLU A 526 O GLN A 531 SHEET 1 AA6 7 PHE B 166 LEU B 168 0 SHEET 2 AA6 7 GLY B 295 LEU B 298 -1 O ILE B 296 N TYR B 167 SHEET 3 AA6 7 LEU B 275 HIS B 280 -1 N ILE B 279 O TRP B 297 SHEET 4 AA6 7 MET B 266 TYR B 271 -1 N MET B 267 O VAL B 278 SHEET 5 AA6 7 LEU B 196 PHE B 202 -1 N VAL B 197 O LEU B 270 SHEET 6 AA6 7 ILE B 224 HIS B 228 1 O LEU B 225 N GLN B 201 SHEET 7 AA6 7 ILE B 248 GLN B 252 1 O SER B 249 N ILE B 224 SHEET 1 AA7 7 TYR B 353 SER B 357 0 SHEET 2 AA7 7 GLU B 538 PHE B 543 -1 O LEU B 542 N TYR B 353 SHEET 3 AA7 7 LYS B 506 THR B 513 -1 N PHE B 510 O PHE B 543 SHEET 4 AA7 7 LYS B 495 PRO B 500 -1 N ARG B 499 O ALA B 508 SHEET 5 AA7 7 VAL B 394 GLN B 397 -1 N VAL B 395 O MET B 498 SHEET 6 AA7 7 LEU B 437 ILE B 440 1 O ILE B 440 N GLY B 396 SHEET 7 AA7 7 PHE B 477 HIS B 478 1 O HIS B 478 N LEU B 439 SHEET 1 AA8 5 TYR B 353 SER B 357 0 SHEET 2 AA8 5 GLU B 538 PHE B 543 -1 O LEU B 542 N TYR B 353 SHEET 3 AA8 5 LYS B 506 THR B 513 -1 N PHE B 510 O PHE B 543 SHEET 4 AA8 5 PHE B 553 VAL B 555 -1 O PHE B 553 N ILE B 507 SHEET 5 AA8 5 THR B 569 PHE B 570 1 O PHE B 570 N LYS B 554 SHEET 1 AA9 3 GLY B 360 GLN B 363 0 SHEET 2 AA9 3 GLN B 531 ILE B 534 -1 O LEU B 532 N PHE B 362 SHEET 3 AA9 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 -4.68 CISPEP 2 LEU B 576 PRO B 577 0 -2.97 SITE 1 AC1 12 TYR A 204 THR A 261 HIS A 263 LYS A 265 SITE 2 AC1 12 ASN A 283 SER A 399 PRO A 461 HIS A 493 SITE 3 AC1 12 LYS A 495 ASN A 516 HOH A 823 HOH A 927 SITE 1 AC2 7 ILE A 355 GLY A 356 SER A 357 THR A 513 SITE 2 AC2 7 ALA A 515 TRP A 522 GLY A 540 SITE 1 AC3 12 TYR B 204 THR B 261 HIS B 263 LYS B 265 SITE 2 AC3 12 ASN B 283 SER B 399 PRO B 461 HIS B 493 SITE 3 AC3 12 LYS B 495 ASN B 516 HOH B 830 HOH B 953 SITE 1 AC4 7 ILE B 355 GLY B 356 SER B 357 THR B 513 SITE 2 AC4 7 ALA B 515 TRP B 522 GLY B 540 SITE 1 AC5 8 THR B 484 VAL B 555 LYS B 556 VAL B 572 SITE 2 AC5 8 TYR B 574 ASP B 575 LEU B 576 HOH B 829 SITE 1 AC6 8 GLY A 549 ILE B 305 LYS B 311 SER B 312 SITE 2 AC6 8 LYS B 320 HIS B 343 HOH B 887 HOH B 951 CRYST1 50.032 105.817 194.211 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 0.019987 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009450 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005149 0.00000