HEADER HYDROLASE 31-MAR-16 5J3Z TITLE CRYSTAL STRUCTURE OF M2HTDP2-CAT IN COMPLEX WITH A SMALL MOLECULE TITLE 2 INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYROSYL-DNA PHOSPHODIESTERASE 2; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 118-370; COMPND 5 SYNONYM: TYR-DNA PHOSPHODIESTERASE 2,5'-TYROSYL-DNA COMPND 6 PHOSPHODIESTERASE,5'-TYR-DNA PHOSPHODIESTERASE,TRAF AND TNF RECEPTOR- COMPND 7 ASSOCIATED PROTEIN; COMPND 8 EC: 3.1.4.-; COMPND 9 ENGINEERED: YES; COMPND 10 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: TDP2, TTRAP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA2 PLYSS KEYWDS TYROSYL DNA PHOSPHODIESTERASE 2 CATALYTIC DOMAIN, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR P.HORNYAK,L.H.PEARL,K.W.CALDECOTT,A.W.OLIVER REVDAT 3 10-JAN-24 5J3Z 1 LINK REVDAT 2 06-JUL-16 5J3Z 1 JRNL REVDAT 1 04-MAY-16 5J3Z 0 JRNL AUTH P.HORNYAK,T.ASKWITH,S.WALKER,E.KOMULAINEN,M.PARADOWSKI, JRNL AUTH 2 L.E.PENNICOTT,E.J.BARTLETT,N.C.BRISSETT,A.RAOOF,M.WATSON, JRNL AUTH 3 A.M.JORDAN,D.J.OGILVIE,S.E.WARD,J.R.ATACK,L.H.PEARL, JRNL AUTH 4 K.W.CALDECOTT,A.W.OLIVER JRNL TITL MODE OF ACTION OF DNA-COMPETITIVE SMALL MOLECULE INHIBITORS JRNL TITL 2 OF TYROSYL DNA PHOSPHODIESTERASE 2. JRNL REF BIOCHEM.J. V. 473 1869 2016 JRNL REFN ESSN 1470-8728 JRNL PMID 27099339 JRNL DOI 10.1042/BCJ20160180 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.2 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.81 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 51379 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 2611 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.85 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 80.45 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 3113 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2208 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2964 REMARK 3 BIN R VALUE (WORKING SET) : 0.2192 REMARK 3 BIN FREE R VALUE : 0.2518 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.79 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 149 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3889 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 168 REMARK 3 SOLVENT ATOMS : 604 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.69 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.43 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.97390 REMARK 3 B22 (A**2) : -0.27110 REMARK 3 B33 (A**2) : -2.70280 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -2.69230 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.221 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.132 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.117 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.120 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.111 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.934 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 4264 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 5774 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 1971 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 90 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 713 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 4264 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 0 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 546 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : 20 ; 1.000 ; HARMONIC REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 5678 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 0.98 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.38 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 2.78 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|* } REMARK 3 ORIGIN FOR THE GROUP (A): -12.7288 -6.6721 -47.9553 REMARK 3 T TENSOR REMARK 3 T11: -0.0643 T22: -0.0513 REMARK 3 T33: -0.0227 T12: 0.0095 REMARK 3 T13: 0.0065 T23: 0.0040 REMARK 3 L TENSOR REMARK 3 L11: 1.1328 L22: 0.9773 REMARK 3 L33: 0.6464 L12: 0.0831 REMARK 3 L13: 0.1063 L23: -0.0683 REMARK 3 S TENSOR REMARK 3 S11: -0.0039 S12: -0.0736 S13: 0.0188 REMARK 3 S21: 0.0260 S22: -0.0017 S23: -0.0301 REMARK 3 S31: 0.0306 S32: 0.0931 S33: 0.0056 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { B|* } REMARK 3 ORIGIN FOR THE GROUP (A): -16.4959 -6.3087 -4.9932 REMARK 3 T TENSOR REMARK 3 T11: -0.0747 T22: -0.0441 REMARK 3 T33: -0.0260 T12: -0.0050 REMARK 3 T13: -0.0066 T23: -0.0184 REMARK 3 L TENSOR REMARK 3 L11: 1.3285 L22: 1.1585 REMARK 3 L33: 0.6430 L12: -0.0110 REMARK 3 L13: 0.1489 L23: -0.3835 REMARK 3 S TENSOR REMARK 3 S11: -0.0029 S12: -0.0645 S13: -0.0777 REMARK 3 S21: -0.0199 S22: 0.0196 S23: -0.0924 REMARK 3 S31: 0.0271 S32: -0.0309 S33: -0.0167 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5J3Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-APR-16. REMARK 100 THE DEPOSITION ID IS D_1000219919. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-OCT-13 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 : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51393 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 42.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 2.900 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 79.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : 0.16600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 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: 4GYZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS PROPANE PH 7.5, 0.2 M REMARK 280 SODIUM CITRATE, 20% W/V PEG3350, 0.3% V/V DMSO, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K 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 21.40000 REMARK 290 SMTRY3 2 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 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 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 115 REMARK 465 ASN A 116 REMARK 465 ALA A 117 REMARK 465 LEU A 118 REMARK 465 GLU A 119 REMARK 465 ASP A 120 REMARK 465 SER A 121 REMARK 465 SER B 115 REMARK 465 ASN B 116 REMARK 465 ALA B 117 REMARK 465 LEU B 118 REMARK 465 GLU B 119 REMARK 465 ASP B 120 REMARK 465 GLU B 333 REMARK 465 GLU B 334 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 SER A 122 OG REMARK 470 ARG A 278 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 310 CG CD CE NZ REMARK 470 GLU A 333 CG CD OE1 OE2 REMARK 470 ASN A 367 CG OD1 ND2 REMARK 470 LYS B 173 CE NZ REMARK 470 THR B 179 OG1 CG2 REMARK 470 LYS B 252 CD CE NZ REMARK 470 LYS B 310 CD CE NZ REMARK 470 GLU B 348 CG CD OE1 OE2 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 ALA A 175 47.17 -145.72 REMARK 500 GLU A 238 121.16 -38.25 REMARK 500 THR A 240 140.03 78.98 REMARK 500 THR A 240 139.77 78.98 REMARK 500 HIS A 243 35.93 -98.65 REMARK 500 ASN A 274 17.30 59.02 REMARK 500 ASP A 277 -129.02 47.05 REMARK 500 ARG A 324 71.15 -112.34 REMARK 500 HIS A 336 -128.20 -102.40 REMARK 500 SER B 154 58.30 38.73 REMARK 500 GLU B 238 122.87 -38.14 REMARK 500 THR B 240 146.78 74.31 REMARK 500 ARG B 324 70.51 -105.81 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 789 DISTANCE = 5.92 ANGSTROMS REMARK 525 HOH B 790 DISTANCE = 6.33 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 132 OD1 REMARK 620 2 GLU A 162 OE1 124.1 REMARK 620 3 HOH A 501 O 68.5 57.5 REMARK 620 4 HOH A 502 O 148.8 82.7 140.3 REMARK 620 5 HOH A 510 O 90.9 96.0 112.0 68.8 REMARK 620 6 HOH A 535 O 80.3 155.4 146.4 73.1 79.5 REMARK 620 7 HOH A 715 O 130.5 72.6 96.9 68.5 136.7 94.1 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 132 OD1 REMARK 620 2 GLU B 162 OE1 101.4 REMARK 620 3 HOH B 508 O 94.5 95.0 REMARK 620 4 HOH B 531 O 75.7 83.5 169.5 REMARK 620 5 HOH B 669 O 82.4 173.1 79.0 103.1 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 6FQ A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 411 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 412 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 413 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 414 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 415 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 416 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 6FQ B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT B 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT B 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT B 411 REMARK 800 REMARK 800 SITE_IDENTIFIER: AF1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT B 412 REMARK 800 REMARK 800 SITE_IDENTIFIER: AF2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT B 413 DBREF 5J3Z A 118 370 UNP Q9JJX7 TYDP2_MOUSE 118 370 DBREF 5J3Z B 118 370 UNP Q9JJX7 TYDP2_MOUSE 118 370 SEQADV 5J3Z SER A 115 UNP Q9JJX7 EXPRESSION TAG SEQADV 5J3Z ASN A 116 UNP Q9JJX7 EXPRESSION TAG SEQADV 5J3Z ALA A 117 UNP Q9JJX7 EXPRESSION TAG SEQADV 5J3Z GLY A 242 UNP Q9JJX7 GLU 242 ENGINEERED MUTATION SEQADV 5J3Z ARG A 278 UNP Q9JJX7 GLN 278 ENGINEERED MUTATION SEQADV 5J3Z CYS A 321 UNP Q9JJX7 TYR 321 ENGINEERED MUTATION SEQADV 5J3Z LEU A 323 UNP Q9JJX7 HIS 323 ENGINEERED MUTATION SEQADV 5J3Z SER B 115 UNP Q9JJX7 EXPRESSION TAG SEQADV 5J3Z ASN B 116 UNP Q9JJX7 EXPRESSION TAG SEQADV 5J3Z ALA B 117 UNP Q9JJX7 EXPRESSION TAG SEQADV 5J3Z GLY B 242 UNP Q9JJX7 GLU 242 ENGINEERED MUTATION SEQADV 5J3Z ARG B 278 UNP Q9JJX7 GLN 278 ENGINEERED MUTATION SEQADV 5J3Z CYS B 321 UNP Q9JJX7 TYR 321 ENGINEERED MUTATION SEQADV 5J3Z LEU B 323 UNP Q9JJX7 HIS 323 ENGINEERED MUTATION SEQRES 1 A 256 SER ASN ALA LEU GLU ASP SER SER THR ILE SER PHE ILE SEQRES 2 A 256 THR TRP ASN ILE ASP GLY LEU ASP GLY CYS ASN LEU PRO SEQRES 3 A 256 GLU ARG ALA ARG GLY VAL CYS SER CYS LEU ALA LEU TYR SEQRES 4 A 256 SER PRO ASP VAL VAL PHE LEU GLN GLU VAL ILE PRO PRO SEQRES 5 A 256 TYR CYS ALA TYR LEU LYS LYS ARG ALA ALA SER TYR THR SEQRES 6 A 256 ILE ILE THR GLY ASN GLU GLU GLY TYR PHE THR ALA ILE SEQRES 7 A 256 LEU LEU LYS LYS GLY ARG VAL LYS PHE LYS SER GLN GLU SEQRES 8 A 256 ILE ILE PRO PHE PRO ASN THR LYS MET MET ARG ASN LEU SEQRES 9 A 256 LEU CYS VAL ASN VAL SER LEU GLY GLY ASN GLU PHE CYS SEQRES 10 A 256 LEU MET THR SER HIS LEU GLU SER THR ARG GLY HIS SER SEQRES 11 A 256 ALA GLU ARG ILE ARG GLN LEU LYS THR VAL LEU GLY LYS SEQRES 12 A 256 MET GLN GLU ALA PRO ASP SER THR THR VAL ILE PHE ALA SEQRES 13 A 256 GLY ASP THR ASN LEU ARG ASP ARG GLU VAL ILE LYS CYS SEQRES 14 A 256 GLY GLY LEU PRO ASP ASN VAL PHE ASP ALA TRP GLU PHE SEQRES 15 A 256 LEU GLY LYS PRO LYS HIS CYS GLN TYR THR TRP ASP THR SEQRES 16 A 256 LYS ALA ASN ASN ASN LEU ARG ILE PRO ALA ALA CYS LYS SEQRES 17 A 256 LEU ARG PHE ASP ARG ILE PHE PHE ARG ALA GLU GLU GLY SEQRES 18 A 256 HIS LEU ILE PRO GLN SER LEU ASP LEU VAL GLY LEU GLU SEQRES 19 A 256 LYS LEU ASP CYS GLY ARG PHE PRO SER ASP HIS TRP GLY SEQRES 20 A 256 LEU LEU CYS THR LEU ASN VAL VAL LEU SEQRES 1 B 256 SER ASN ALA LEU GLU ASP SER SER THR ILE SER PHE ILE SEQRES 2 B 256 THR TRP ASN ILE ASP GLY LEU ASP GLY CYS ASN LEU PRO SEQRES 3 B 256 GLU ARG ALA ARG GLY VAL CYS SER CYS LEU ALA LEU TYR SEQRES 4 B 256 SER PRO ASP VAL VAL PHE LEU GLN GLU VAL ILE PRO PRO SEQRES 5 B 256 TYR CYS ALA TYR LEU LYS LYS ARG ALA ALA SER TYR THR SEQRES 6 B 256 ILE ILE THR GLY ASN GLU GLU GLY TYR PHE THR ALA ILE SEQRES 7 B 256 LEU LEU LYS LYS GLY ARG VAL LYS PHE LYS SER GLN GLU SEQRES 8 B 256 ILE ILE PRO PHE PRO ASN THR LYS MET MET ARG ASN LEU SEQRES 9 B 256 LEU CYS VAL ASN VAL SER LEU GLY GLY ASN GLU PHE CYS SEQRES 10 B 256 LEU MET THR SER HIS LEU GLU SER THR ARG GLY HIS SER SEQRES 11 B 256 ALA GLU ARG ILE ARG GLN LEU LYS THR VAL LEU GLY LYS SEQRES 12 B 256 MET GLN GLU ALA PRO ASP SER THR THR VAL ILE PHE ALA SEQRES 13 B 256 GLY ASP THR ASN LEU ARG ASP ARG GLU VAL ILE LYS CYS SEQRES 14 B 256 GLY GLY LEU PRO ASP ASN VAL PHE ASP ALA TRP GLU PHE SEQRES 15 B 256 LEU GLY LYS PRO LYS HIS CYS GLN TYR THR TRP ASP THR SEQRES 16 B 256 LYS ALA ASN ASN ASN LEU ARG ILE PRO ALA ALA CYS LYS SEQRES 17 B 256 LEU ARG PHE ASP ARG ILE PHE PHE ARG ALA GLU GLU GLY SEQRES 18 B 256 HIS LEU ILE PRO GLN SER LEU ASP LEU VAL GLY LEU GLU SEQRES 19 B 256 LYS LEU ASP CYS GLY ARG PHE PRO SER ASP HIS TRP GLY SEQRES 20 B 256 LEU LEU CYS THR LEU ASN VAL VAL LEU HET 6FQ A 401 29 HET MG A 402 1 HET GOL A 403 6 HET GOL A 404 6 HET EDO A 405 4 HET EDO A 406 4 HET EDO A 407 4 HET EDO A 408 4 HET EDO A 409 4 HET EDO A 410 4 HET EDO A 411 4 HET EDO A 412 4 HET EDO A 413 4 HET EDO A 414 4 HET EDO A 415 4 HET ACT A 416 4 HET 6FQ B 401 29 HET MG B 402 1 HET GOL B 403 6 HET GOL B 404 6 HET EDO B 405 4 HET EDO B 406 4 HET EDO B 407 4 HET EDO B 408 4 HET ACT B 409 4 HET ACT B 410 4 HET ACT B 411 4 HET ACT B 412 4 HET ACT B 413 4 HETNAM 6FQ 2,4-DIOXO-10-[3-(1H-TETRAZOL-5-YL)PHENYL]-2,3,4,10- HETNAM 2 6FQ TETRAHYDROPYRIMIDO[4,5-B]QUINOLINE-8-CARBONITRILE HETNAM MG MAGNESIUM ION HETNAM GOL GLYCEROL HETNAM EDO 1,2-ETHANEDIOL HETNAM ACT ACETATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 6FQ 2(C19 H10 N8 O2) FORMUL 4 MG 2(MG 2+) FORMUL 5 GOL 4(C3 H8 O3) FORMUL 7 EDO 15(C2 H6 O2) FORMUL 18 ACT 6(C2 H3 O2 1-) FORMUL 32 HOH *604(H2 O) HELIX 1 AA1 ASN A 138 SER A 154 1 17 HELIX 2 AA2 ILE A 164 ALA A 175 1 12 HELIX 3 AA3 THR A 240 GLY A 242 5 3 HELIX 4 AA4 HIS A 243 ALA A 261 1 19 HELIX 5 AA5 ARG A 278 GLY A 284 1 7 HELIX 6 AA6 ALA A 293 LEU A 297 1 5 HELIX 7 AA7 PRO A 300 GLN A 304 5 5 HELIX 8 AA8 ASN B 138 SER B 154 1 17 HELIX 9 AA9 ILE B 164 ALA B 175 1 12 HELIX 10 AB1 THR B 240 GLY B 242 5 3 HELIX 11 AB2 HIS B 243 ALA B 261 1 19 HELIX 12 AB3 ARG B 276 GLY B 284 1 9 HELIX 13 AB4 ALA B 293 LEU B 297 1 5 HELIX 14 AB5 PRO B 300 GLN B 304 5 5 SHEET 1 AA1 6 TYR A 178 THR A 182 0 SHEET 2 AA1 6 PHE A 189 LYS A 195 -1 O LEU A 194 N THR A 179 SHEET 3 AA1 6 VAL A 157 VAL A 163 -1 N VAL A 158 O LEU A 193 SHEET 4 AA1 6 THR A 123 ASN A 130 1 N ILE A 127 O PHE A 159 SHEET 5 AA1 6 GLY A 361 VAL A 368 -1 O CYS A 364 N PHE A 126 SHEET 6 AA1 6 LEU A 337 VAL A 345 -1 N GLN A 340 O THR A 365 SHEET 1 AA2 6 LYS A 200 PRO A 208 0 SHEET 2 AA2 6 ASN A 217 LEU A 225 -1 O LEU A 218 N ILE A 207 SHEET 3 AA2 6 ASN A 228 THR A 234 -1 O LEU A 232 N VAL A 221 SHEET 4 AA2 6 THR A 266 ASP A 272 1 O ILE A 268 N MET A 233 SHEET 5 AA2 6 ASP A 326 ARG A 331 -1 O PHE A 329 N PHE A 269 SHEET 6 AA2 6 PHE A 291 ASP A 292 -1 N PHE A 291 O PHE A 330 SHEET 1 AA3 2 TRP A 307 ASP A 308 0 SHEET 2 AA3 2 LYS A 322 LEU A 323 -1 O LEU A 323 N TRP A 307 SHEET 1 AA4 6 TYR B 178 THR B 182 0 SHEET 2 AA4 6 PHE B 189 LYS B 195 -1 O ILE B 192 N ILE B 181 SHEET 3 AA4 6 VAL B 157 VAL B 163 -1 N VAL B 163 O PHE B 189 SHEET 4 AA4 6 SER B 122 ASN B 130 1 N ILE B 127 O PHE B 159 SHEET 5 AA4 6 GLY B 361 VAL B 368 -1 O VAL B 368 N SER B 122 SHEET 6 AA4 6 LEU B 337 VAL B 345 -1 N ASP B 343 O LEU B 363 SHEET 1 AA5 6 LYS B 200 PRO B 208 0 SHEET 2 AA5 6 ASN B 217 LEU B 225 -1 O ASN B 222 N SER B 203 SHEET 3 AA5 6 ASN B 228 THR B 234 -1 O LEU B 232 N VAL B 221 SHEET 4 AA5 6 THR B 266 ASP B 272 1 O ILE B 268 N MET B 233 SHEET 5 AA5 6 ASP B 326 ARG B 331 -1 O PHE B 329 N PHE B 269 SHEET 6 AA5 6 VAL B 290 ASP B 292 -1 N PHE B 291 O PHE B 330 SHEET 1 AA6 2 TRP B 307 ASP B 308 0 SHEET 2 AA6 2 LYS B 322 LEU B 323 -1 O LEU B 323 N TRP B 307 SSBOND 1 CYS A 137 CYS B 137 1555 1555 2.03 SSBOND 2 CYS A 220 CYS A 231 1555 1555 2.07 LINK OD1 ASP A 132 MG MG A 402 1555 1555 2.21 LINK OE1 GLU A 162 MG MG A 402 1555 1555 2.78 LINK MG MG A 402 O HOH A 501 1555 1555 2.56 LINK MG MG A 402 O HOH A 502 1555 1555 2.11 LINK MG MG A 402 O HOH A 510 1555 1555 2.57 LINK MG MG A 402 O HOH A 535 1555 1555 2.40 LINK MG MG A 402 O HOH A 715 1555 1555 2.65 LINK OD1 ASP B 132 MG MG B 402 1555 1555 2.32 LINK OE1 GLU B 162 MG MG B 402 1555 1555 2.27 LINK MG MG B 402 O HOH B 508 1555 1555 2.37 LINK MG MG B 402 O HOH B 531 1555 1555 2.10 LINK MG MG B 402 O HOH B 669 1555 1555 2.46 CISPEP 1 GLY B 335 HIS B 336 0 1.21 SITE 1 AC1 12 THR A 240 ARG A 241 ARG A 276 ILE A 317 SITE 2 AC1 12 CYS A 321 LEU A 323 HOH A 534 HOH A 625 SITE 3 AC1 12 HOH A 648 ILE B 317 PRO B 318 6FQ B 401 SITE 1 AC2 8 ASP A 132 GLU A 162 HOH A 501 HOH A 502 SITE 2 AC2 8 HOH A 510 HOH A 535 HOH A 715 ARG B 316 SITE 1 AC3 10 TRP A 307 ASP A 358 HIS A 359 EDO A 409 SITE 2 AC3 10 HOH A 502 HOH A 535 HOH A 563 HOH A 679 SITE 3 AC3 10 PRO B 318 HOH B 572 SITE 1 AC4 4 GLY A 256 GLN A 259 PRO A 287 HOH A 657 SITE 1 AC5 5 VAL A 199 LYS A 200 PHE A 201 HOH A 569 SITE 2 AC5 5 HOH A 583 SITE 1 AC6 8 LYS A 301 HIS A 302 GLN A 304 TYR A 305 SITE 2 AC6 8 ASP A 308 LEU A 344 TRP A 360 HOH A 550 SITE 1 AC7 9 ASN A 184 GLU A 186 TYR A 188 PHE A 189 SITE 2 AC7 9 MET A 214 MET A 215 HOH A 522 HOH A 605 SITE 3 AC7 9 HOH A 699 SITE 1 AC8 6 ASP A 156 ARG A 198 EDO A 410 EDO A 411 SITE 2 AC8 6 HOH A 514 HOH A 562 SITE 1 AC9 9 ASN A 130 GLU A 162 HIS A 236 SER A 239 SITE 2 AC9 9 ASP A 272 ASN A 274 HIS A 359 GOL A 403 SITE 3 AC9 9 HOH A 579 SITE 1 AD1 5 THR A 123 ASP A 156 GLY A 226 EDO A 408 SITE 2 AD1 5 HOH A 612 SITE 1 AD2 3 EDO A 408 HOH A 606 HOH A 669 SITE 1 AD3 3 HOH A 515 HOH A 539 HOH A 551 SITE 1 AD4 4 ARG A 241 SER A 244 ASP A 277 GLU A 279 SITE 1 AD5 6 HIS A 302 SER A 341 LEU A 342 ASP A 343 SITE 2 AD5 6 HOH A 548 HOH A 559 SITE 1 AD6 4 ASN A 289 PHE A 291 ALA A 332 GLU A 334 SITE 1 AD7 2 LEU A 152 HOH A 529 SITE 1 AD8 13 ILE A 317 PRO A 318 ALA A 319 6FQ A 401 SITE 2 AD8 13 THR B 240 ARG B 241 ARG B 276 ARG B 278 SITE 3 AD8 13 ILE B 317 CYS B 321 LEU B 323 HOH B 610 SITE 4 AD8 13 HOH B 624 SITE 1 AD9 5 ASP B 132 GLU B 162 HOH B 508 HOH B 531 SITE 2 AD9 5 HOH B 669 SITE 1 AE1 5 ASN B 211 ARG B 249 GOL B 404 HOH B 517 SITE 2 AE1 5 HOH B 539 SITE 1 AE2 8 PHE B 209 PRO B 210 ASN B 211 GLU B 246 SITE 2 AE2 8 ARG B 249 THR B 253 GOL B 403 HOH B 540 SITE 1 AE3 8 LYS B 301 HIS B 302 GLN B 304 TYR B 305 SITE 2 AE3 8 ASP B 308 LEU B 344 TRP B 360 HOH B 695 SITE 1 AE4 5 CYS B 149 TYR B 153 GLY B 346 LEU B 347 SITE 2 AE4 5 HOH B 576 SITE 1 AE5 3 LYS B 257 GLU B 260 HOH B 646 SITE 1 AE6 7 ASP B 277 TRP B 294 GLN B 304 TYR B 305 SITE 2 AE6 7 ARG B 324 HOH B 536 HOH B 567 SITE 1 AE7 4 GLY B 197 VAL B 199 HOH B 522 HOH B 574 SITE 1 AE8 6 ILE B 180 ILE B 181 THR B 182 GLU B 185 SITE 2 AE8 6 HOH B 501 HOH B 598 SITE 1 AE9 3 GLY B 197 HOH B 603 HOH B 687 SITE 1 AF1 4 TRP B 307 ASP B 358 HIS B 359 HOH B 504 SITE 1 AF2 1 TYR B 170 CRYST1 61.010 42.800 108.760 90.00 94.15 90.00 P 1 21 1 4 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 0.016391 0.000000 0.001189 0.00000 SCALE2 0.000000 0.023364 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009219 0.00000