HEADER DNA BINDING PROTEIN, HYDROLASE/INHIBITOR11-MAR-20 6W4R TITLE STRUCTURE OF TDP1 CATALYTIC DOMAIN IN COMPLEX WITH INHIBITOR XZ633P 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-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 2 18-OCT-23 6W4R 1 REMARK REVDAT 1 17-MAR-21 6W4R 0 JRNL AUTH G.T.LOUNTOS,D.S.WAUGH JRNL TITL TDP1 CATALYTIC DOMAIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.82 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) : 1.82 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.16 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 90975 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 : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.880 REMARK 3 FREE R VALUE TEST SET COUNT : 4438 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 48.1640 - 5.6505 1.00 3196 166 0.1733 0.1630 REMARK 3 2 5.6505 - 4.4860 0.99 3017 161 0.1403 0.1571 REMARK 3 3 4.4860 - 3.9193 1.00 3028 143 0.1360 0.1538 REMARK 3 4 3.9193 - 3.5610 1.00 2977 148 0.1592 0.1780 REMARK 3 5 3.5610 - 3.3059 1.00 2994 134 0.1719 0.1998 REMARK 3 6 3.3059 - 3.1110 1.00 2942 170 0.1788 0.2272 REMARK 3 7 3.1110 - 2.9552 1.00 2960 159 0.1928 0.2739 REMARK 3 8 2.9552 - 2.8266 1.00 2984 148 0.1916 0.1992 REMARK 3 9 2.8266 - 2.7178 1.00 2908 155 0.1900 0.2263 REMARK 3 10 2.7178 - 2.6240 1.00 2954 135 0.1816 0.2303 REMARK 3 11 2.6240 - 2.5420 1.00 2937 140 0.1906 0.2350 REMARK 3 12 2.5420 - 2.4693 0.99 2909 146 0.1916 0.2377 REMARK 3 13 2.4693 - 2.4043 1.00 2924 158 0.1890 0.2420 REMARK 3 14 2.4043 - 2.3456 1.00 2897 160 0.1932 0.2357 REMARK 3 15 2.3456 - 2.2923 1.00 2907 152 0.1939 0.2583 REMARK 3 16 2.2923 - 2.2435 1.00 2910 163 0.2027 0.2363 REMARK 3 17 2.2435 - 2.1987 1.00 2899 148 0.1956 0.2348 REMARK 3 18 2.1987 - 2.1572 1.00 2871 162 0.1921 0.2041 REMARK 3 19 2.1572 - 2.1186 1.00 2970 137 0.2022 0.2540 REMARK 3 20 2.1186 - 2.0827 1.00 2876 160 0.2031 0.2307 REMARK 3 21 2.0827 - 2.0491 1.00 2917 153 0.2021 0.2498 REMARK 3 22 2.0491 - 2.0176 1.00 2936 140 0.2211 0.3002 REMARK 3 23 2.0176 - 1.9879 1.00 2851 141 0.2169 0.2642 REMARK 3 24 1.9879 - 1.9599 1.00 2948 149 0.2154 0.2402 REMARK 3 25 1.9599 - 1.9334 0.99 2889 146 0.2215 0.2504 REMARK 3 26 1.9334 - 1.9083 0.98 2819 132 0.2176 0.2594 REMARK 3 27 1.9083 - 1.8845 0.95 2775 144 0.2144 0.2617 REMARK 3 28 1.8845 - 1.8618 0.91 2646 133 0.2226 0.2555 REMARK 3 29 1.8618 - 1.8401 0.86 2438 130 0.2218 0.2553 REMARK 3 30 1.8401 - 1.8195 0.77 2258 125 0.2451 0.3200 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) : 20.930 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.15 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 6W4R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1000247222. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-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 : DENZO REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 92596 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.819 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.10300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.82 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : 0.93500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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 (%): 49.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 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 24.85950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 97.05250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 52.81200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 97.05250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.85950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 52.81200 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 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 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 A 344 CG CD CE NZ REMARK 470 MET A 567 CG SD CE 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 NZ LYS B 506 O HOH B 801 1.86 REMARK 500 O HOH A 885 O HOH A 1042 2.06 REMARK 500 O HOH A 1109 O HOH A 1121 2.15 REMARK 500 O HOH A 951 O HOH A 1100 2.16 REMARK 500 O HOH A 802 O HOH A 906 2.18 REMARK 500 OD1 ASN A 528 O HOH A 801 2.18 REMARK 500 O HOH A 888 O HOH A 1102 2.19 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 ARG A 232 -126.77 51.20 REMARK 500 HIS A 290 -68.14 -94.27 REMARK 500 TRP A 411 -46.44 -155.20 REMARK 500 GLN A 470 47.82 -146.72 REMARK 500 ALA A 482 45.87 -148.56 REMARK 500 PHE A 504 19.16 59.94 REMARK 500 MET A 567 0.95 -45.99 REMARK 500 ALA A 568 32.87 -86.56 REMARK 500 ARG B 232 -123.18 48.03 REMARK 500 HIS B 290 -71.15 -97.52 REMARK 500 TRP B 411 -48.69 -165.41 REMARK 500 SER B 414 -74.88 -69.94 REMARK 500 GLN B 470 50.24 -149.10 REMARK 500 ALA B 482 47.92 -144.58 REMARK 500 PHE B 504 19.94 57.71 REMARK 500 MET B 567 24.56 -65.93 REMARK 500 ALA B 568 35.69 -85.58 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 A1228 DISTANCE = 6.13 ANGSTROMS REMARK 525 HOH A1229 DISTANCE = 6.19 ANGSTROMS REMARK 525 HOH A1230 DISTANCE = 6.68 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MPO A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SZV A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 704 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SZV B 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 704 DBREF 6W4R A 148 608 UNP Q9NUW8 TYDP1_HUMAN 148 608 DBREF 6W4R 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 MPO A 701 13 HET SZV A 702 29 HET EDO A 703 4 HET EDO A 704 4 HET SZV B 701 29 HET EDO B 702 4 HET EDO B 703 4 HET EDO B 704 4 HETNAM MPO 3[N-MORPHOLINO]PROPANE SULFONIC ACID HETNAM SZV 4-{[2-(2-HYDROXYPHENYL)IMIDAZO[1,2-A]PYRAZIN-3- HETNAM 2 SZV YL]AMINO}BENZENE-1,2-DICARBOXYLIC ACID HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 MPO C7 H15 N O4 S FORMUL 4 SZV 2(C20 H14 N4 O5) FORMUL 5 EDO 5(C2 H6 O2) FORMUL 11 HOH *698(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 GLU A 415 THR A 422 1 8 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 LEU B 421 1 7 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 LYS B 469 1 7 HELIX 37 AE1 GLN B 470 SER B 475 5 6 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 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 VAL A 395 O MET A 498 SHEET 6 AA3 7 LEU A 437 ILE A 440 1 O ILE A 440 N GLY A 396 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 LEU B 269 O ARG B 276 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 CYS B 251 N LEU B 226 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 TYR B 438 N VAL B 394 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 -4.96 CISPEP 2 LEU B 576 PRO B 577 0 -4.51 SITE 1 AC1 10 HIS A 263 SER A 400 VAL A 401 PRO A 461 SITE 2 AC1 10 SER A 518 ALA A 520 SZV A 702 HOH A 956 SITE 3 AC1 10 HOH A 959 HOH A 994 SITE 1 AC2 15 TYR A 204 THR A 261 HIS A 263 LYS A 265 SITE 2 AC2 15 ASN A 283 SER A 399 PRO A 461 HIS A 493 SITE 3 AC2 15 LYS A 495 ASN A 516 MPO A 701 HOH A 894 SITE 4 AC2 15 HOH A1006 HOH A1013 HOH A1086 SITE 1 AC3 7 ILE A 355 GLY A 356 SER A 357 THR A 513 SITE 2 AC3 7 ALA A 515 TRP A 522 GLY A 540 SITE 1 AC4 4 ASP A 322 ASN A 369 ARG A 374 HOH A 933 SITE 1 AC5 13 TYR B 204 THR B 261 HIS B 263 LYS B 265 SITE 2 AC5 13 ASN B 283 SER B 399 PRO B 461 HIS B 493 SITE 3 AC5 13 LYS B 495 ASN B 516 HOH B 828 HOH B 840 SITE 4 AC5 13 HOH B 882 SITE 1 AC6 7 ILE B 355 GLY B 356 SER B 357 THR B 513 SITE 2 AC6 7 ALA B 515 TRP B 522 GLY B 540 SITE 1 AC7 5 THR B 484 LYS B 556 GLN B 557 TYR B 574 SITE 2 AC7 5 LEU B 576 SITE 1 AC8 7 GLY A 549 ILE B 305 LYS B 311 SER B 312 SITE 2 AC8 7 LYS B 320 HIS B 343 HOH B1003 CRYST1 49.719 105.624 194.105 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 0.020113 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009468 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005152 0.00000