HEADER OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR 21-JUN-18 6DUM TITLE ALDH1A1 N121S IN COMPLEX WITH 6-{[(3-FLUOROPHENYL)METHYL]SULFANYL}-2- TITLE 2 (OXETAN-3-YL)-5-PHENYL-2,5-DIHYDRO-4H-PYRAZOLO[3,4-D]PYRIMIDIN-4-ONE TITLE 3 (COMPOUND 13G) COMPND MOL_ID: 1; COMPND 2 MOLECULE: RETINAL DEHYDROGENASE 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RALDH1, ALDH-E1, ALHDII, ALDEHYDE DEHYDROGENASE FAMILY 1 COMPND 5 MEMBER A1, ALDEHYDE DEHYDROGENASE, CYTOSOLIC; COMPND 6 EC: 1.2.1.-,1.2.1.36; COMPND 7 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: ALDH1A1, ALDC, ALDH1, PUMB1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS OXIDOREDUCTASE, OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.D.BUCHMAN,T.D.HURLEY REVDAT 3 13-MAR-24 6DUM 1 LINK REVDAT 2 04-DEC-19 6DUM 1 REMARK REVDAT 1 01-MAY-19 6DUM 0 JRNL AUTH B.C.HUDDLE,E.GRIMLEY,C.D.BUCHMAN,M.CHTCHERBININE,B.DEBNATH, JRNL AUTH 2 P.MEHTA,K.YANG,C.A.MORGAN,S.LI,J.FELTON,D.SUN,G.MEHTA, JRNL AUTH 3 N.NEAMATI,R.J.BUCKANOVICH,T.D.HURLEY,S.D.LARSEN JRNL TITL STRUCTURE-BASED OPTIMIZATION OF A NOVEL CLASS OF ALDEHYDE JRNL TITL 2 DEHYDROGENASE 1A (ALDH1A) SUBFAMILY-SELECTIVE INHIBITORS AS JRNL TITL 3 POTENTIAL ADJUNCTS TO OVARIAN CANCER CHEMOTHERAPY. JRNL REF J.MED.CHEM. V. 61 8754 2018 JRNL REFN ISSN 0022-2623 JRNL PMID 30221940 JRNL DOI 10.1021/ACS.JMEDCHEM.8B00930 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 31637 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) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1690 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1979 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 83.95 REMARK 3 BIN R VALUE (WORKING SET) : 0.3060 REMARK 3 BIN FREE R VALUE SET COUNT : 102 REMARK 3 BIN FREE R VALUE : 0.3080 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3814 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 82 REMARK 3 SOLVENT ATOMS : 172 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.71 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.38000 REMARK 3 B22 (A**2) : -3.38000 REMARK 3 B33 (A**2) : 6.76000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.205 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.183 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.218 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 15.824 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.934 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3990 ; 0.010 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3783 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5394 ; 1.473 ; 1.985 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8735 ; 0.766 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 493 ; 6.322 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 165 ;37.811 ;24.727 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 672 ;14.834 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;16.841 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 593 ; 0.070 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4472 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 883 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 8 A 59 REMARK 3 ORIGIN FOR THE GROUP (A): 51.9712 -32.1197 28.2646 REMARK 3 T TENSOR REMARK 3 T11: 0.2040 T22: 0.0319 REMARK 3 T33: 0.4179 T12: 0.0369 REMARK 3 T13: 0.2036 T23: 0.0717 REMARK 3 L TENSOR REMARK 3 L11: 5.0031 L22: 1.0873 REMARK 3 L33: 2.5855 L12: 0.6682 REMARK 3 L13: 0.5269 L23: -0.8445 REMARK 3 S TENSOR REMARK 3 S11: -0.1634 S12: -0.1905 S13: -0.4976 REMARK 3 S21: 0.1206 S22: -0.0115 S23: 0.1472 REMARK 3 S31: 0.3935 S32: 0.0183 S33: 0.1750 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 60 A 271 REMARK 3 ORIGIN FOR THE GROUP (A): 55.9218 -16.8777 17.3466 REMARK 3 T TENSOR REMARK 3 T11: 0.0364 T22: 0.0159 REMARK 3 T33: 0.3248 T12: 0.0186 REMARK 3 T13: 0.0536 T23: 0.0181 REMARK 3 L TENSOR REMARK 3 L11: 1.1161 L22: 1.1638 REMARK 3 L33: 0.6278 L12: 0.6998 REMARK 3 L13: -0.5660 L23: -0.4406 REMARK 3 S TENSOR REMARK 3 S11: -0.1080 S12: -0.0832 S13: -0.0819 REMARK 3 S21: 0.0513 S22: -0.0361 S23: 0.1409 REMARK 3 S31: 0.0336 S32: 0.0203 S33: 0.1441 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 272 A 501 REMARK 3 ORIGIN FOR THE GROUP (A): 31.3055 -9.3149 19.9136 REMARK 3 T TENSOR REMARK 3 T11: 0.0583 T22: 0.0551 REMARK 3 T33: 0.4508 T12: 0.0224 REMARK 3 T13: 0.0883 T23: -0.0356 REMARK 3 L TENSOR REMARK 3 L11: 0.9787 L22: 1.0347 REMARK 3 L33: 0.8101 L12: 0.4779 REMARK 3 L13: -0.5144 L23: -0.6729 REMARK 3 S TENSOR REMARK 3 S11: -0.1275 S12: -0.0751 S13: -0.0724 REMARK 3 S21: 0.1063 S22: 0.0801 S23: 0.2644 REMARK 3 S31: 0.0237 S32: -0.1144 S33: 0.0473 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 6DUM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1000235262. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-MAR-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.2-6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33340 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 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 (%) : 97.2 REMARK 200 DATA REDUNDANCY : 12.60 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.6 REMARK 200 DATA REDUNDANCY IN SHELL : 12.00 REMARK 200 R MERGE FOR SHELL (I) : 0.31600 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: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM BIS-TRIS, PH 6.2-6.5, 200 MM REMARK 280 SODIUM CHLORIDE, 5 MM YTTERBIUM CHLORIDE, 6-11% PEG3350, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 300K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 4 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 29950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 57790 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -363.0 KCAL/MOL 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 BIOMT1 2 -1.000000 0.000000 0.000000 108.80200 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 108.80200 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 CL CL A 608 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 868 LIES ON A SPECIAL POSITION. 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 MET A 1 REMARK 465 SER A 2 REMARK 465 SER A 3 REMARK 465 SER A 4 REMARK 465 GLY A 5 REMARK 465 THR A 6 REMARK 465 PRO A 7 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 815 O HOH A 838 1.61 REMARK 500 O HOH A 747 O HOH A 838 1.85 REMARK 500 O HOH A 747 O HOH A 815 1.97 REMARK 500 YB YB A 601 O HOH A 815 1.99 REMARK 500 O HOH A 780 O HOH A 859 2.05 REMARK 500 O HOH A 815 O HOH A 819 2.08 REMARK 500 O HOH A 825 O HOH A 866 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OE2 GLU A 28 OG1 THR A 337 4655 2.07 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 THR A 228 -81.36 -102.22 REMARK 500 SER A 261 -85.18 -99.50 REMARK 500 LEU A 270 -153.77 -124.93 REMARK 500 GLN A 301 51.57 -100.25 REMARK 500 TYR A 380 59.59 -95.00 REMARK 500 LYS A 470 -143.11 53.60 REMARK 500 LEU A 478 177.23 70.01 REMARK 500 REMARK 500 REMARK: NULL 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 YB A 601 YB REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 747 O REMARK 620 2 HOH A 819 O 86.5 REMARK 620 3 HOH A 825 O 84.9 66.3 REMARK 620 4 HOH A 838 O 50.1 85.4 128.8 REMARK 620 5 HOH A 851 O 135.5 80.6 126.4 86.3 REMARK 620 6 HOH A 858 O 81.6 164.1 122.6 78.9 100.6 REMARK 620 7 HOH A 858 O 141.7 108.5 70.6 160.4 82.5 87.3 REMARK 620 8 HOH A 866 O 126.2 46.8 55.8 128.7 70.7 148.6 62.0 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 YB A 602 YB REMARK 620 N RES CSSEQI ATOM REMARK 620 1 NAI A 604 O2A REMARK 620 2 NAI A 604 O1N 59.8 REMARK 620 3 HOH A 701 O 65.3 66.1 REMARK 620 4 HOH A 780 O 95.7 147.4 84.7 REMARK 620 5 HOH A 842 O 82.3 113.9 142.6 80.3 REMARK 620 6 HOH A 859 O 144.3 154.6 124.4 55.7 72.8 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue YB A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue YB A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue A5Y A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAI A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 606 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 607 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 609 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 610 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 611 DBREF 6DUM A 1 501 UNP V9HW83 V9HW83_HUMAN 1 501 SEQADV 6DUM SER A 121 UNP V9HW83 ASN 121 CONFLICT SEQRES 1 A 501 MET SER SER SER GLY THR PRO ASP LEU PRO VAL LEU LEU SEQRES 2 A 501 THR ASP LEU LYS ILE GLN TYR THR LYS ILE PHE ILE ASN SEQRES 3 A 501 ASN GLU TRP HIS ASP SER VAL SER GLY LYS LYS PHE PRO SEQRES 4 A 501 VAL PHE ASN PRO ALA THR GLU GLU GLU LEU CYS GLN VAL SEQRES 5 A 501 GLU GLU GLY ASP LYS GLU ASP VAL ASP LYS ALA VAL LYS SEQRES 6 A 501 ALA ALA ARG GLN ALA PHE GLN ILE GLY SER PRO TRP ARG SEQRES 7 A 501 THR MET ASP ALA SER GLU ARG GLY ARG LEU LEU TYR LYS SEQRES 8 A 501 LEU ALA ASP LEU ILE GLU ARG ASP ARG LEU LEU LEU ALA SEQRES 9 A 501 THR MET GLU SER MET ASN GLY GLY LYS LEU TYR SER ASN SEQRES 10 A 501 ALA TYR LEU SER ASP LEU ALA GLY CYS ILE LYS THR LEU SEQRES 11 A 501 ARG TYR CYS ALA GLY TRP ALA ASP LYS ILE GLN GLY ARG SEQRES 12 A 501 THR ILE PRO ILE ASP GLY ASN PHE PHE THR TYR THR ARG SEQRES 13 A 501 HIS GLU PRO ILE GLY VAL CYS GLY GLN ILE ILE PRO TRP SEQRES 14 A 501 ASN PHE PRO LEU VAL MET LEU ILE TRP LYS ILE GLY PRO SEQRES 15 A 501 ALA LEU SER CYS GLY ASN THR VAL VAL VAL LYS PRO ALA SEQRES 16 A 501 GLU GLN THR PRO LEU THR ALA LEU HIS VAL ALA SER LEU SEQRES 17 A 501 ILE LYS GLU ALA GLY PHE PRO PRO GLY VAL VAL ASN ILE SEQRES 18 A 501 VAL PRO GLY TYR GLY PRO THR ALA GLY ALA ALA ILE SER SEQRES 19 A 501 SER HIS MET ASP ILE ASP LYS VAL ALA PHE THR GLY SER SEQRES 20 A 501 THR GLU VAL GLY LYS LEU ILE LYS GLU ALA ALA GLY LYS SEQRES 21 A 501 SER ASN LEU LYS ARG VAL THR LEU GLU LEU GLY GLY LYS SEQRES 22 A 501 SER PRO CYS ILE VAL LEU ALA ASP ALA ASP LEU ASP ASN SEQRES 23 A 501 ALA VAL GLU PHE ALA HIS HIS GLY VAL PHE TYR HIS GLN SEQRES 24 A 501 GLY GLN CYS CYS ILE ALA ALA SER ARG ILE PHE VAL GLU SEQRES 25 A 501 GLU SER ILE TYR ASP GLU PHE VAL ARG ARG SER VAL GLU SEQRES 26 A 501 ARG ALA LYS LYS TYR ILE LEU GLY ASN PRO LEU THR PRO SEQRES 27 A 501 GLY VAL THR GLN GLY PRO GLN ILE ASP LYS GLU GLN TYR SEQRES 28 A 501 ASP LYS ILE LEU ASP LEU ILE GLU SER GLY LYS LYS GLU SEQRES 29 A 501 GLY ALA LYS LEU GLU CYS GLY GLY GLY PRO TRP GLY ASN SEQRES 30 A 501 LYS GLY TYR PHE VAL GLN PRO THR VAL PHE SER ASN VAL SEQRES 31 A 501 THR ASP GLU MET ARG ILE ALA LYS GLU GLU ILE PHE GLY SEQRES 32 A 501 PRO VAL GLN GLN ILE MET LYS PHE LYS SER LEU ASP ASP SEQRES 33 A 501 VAL ILE LYS ARG ALA ASN ASN THR PHE TYR GLY LEU SER SEQRES 34 A 501 ALA GLY VAL PHE THR LYS ASP ILE ASP LYS ALA ILE THR SEQRES 35 A 501 ILE SER SER ALA LEU GLN ALA GLY THR VAL TRP VAL ASN SEQRES 36 A 501 CYS TYR GLY VAL VAL SER ALA GLN CYS PRO PHE GLY GLY SEQRES 37 A 501 PHE LYS MET SER GLY ASN GLY ARG GLU LEU GLY GLU TYR SEQRES 38 A 501 GLY PHE HIS GLU TYR THR GLU VAL LYS THR VAL THR VAL SEQRES 39 A 501 LYS ILE SER GLN LYS ASN SER HET YB A 601 1 HET YB A 602 1 HET A5Y A 603 29 HET NAI A 604 44 HET CL A 605 1 HET CL A 606 1 HET CL A 607 1 HET CL A 608 1 HET CL A 609 1 HET CL A 610 1 HET CL A 611 1 HETNAM YB YTTERBIUM (III) ION HETNAM A5Y 6-{[(3-FLUOROPHENYL)METHYL]SULFANYL}-2-(OXETAN-3-YL)-5- HETNAM 2 A5Y PHENYL-2,5-DIHYDRO-4H-PYRAZOLO[3,4-D]PYRIMIDIN-4-ONE HETNAM NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE HETNAM CL CHLORIDE ION HETSYN NAI NADH FORMUL 2 YB 2(YB 3+) FORMUL 4 A5Y C21 H17 F N4 O2 S FORMUL 5 NAI C21 H29 N7 O14 P2 FORMUL 6 CL 7(CL 1-) FORMUL 13 HOH *172(H2 O) HELIX 1 AA1 ASP A 56 GLN A 72 1 17 HELIX 2 AA2 SER A 75 MET A 80 1 6 HELIX 3 AA3 ASP A 81 ASP A 99 1 19 HELIX 4 AA4 ASP A 99 GLY A 112 1 14 HELIX 5 AA5 LEU A 114 SER A 121 1 8 HELIX 6 AA6 SER A 121 ALA A 137 1 17 HELIX 7 AA7 ASP A 138 ILE A 140 5 3 HELIX 8 AA8 PHE A 171 CYS A 186 1 16 HELIX 9 AA9 PRO A 199 GLY A 213 1 15 HELIX 10 AB1 THR A 228 SER A 235 1 8 HELIX 11 AB2 SER A 247 SER A 261 1 15 HELIX 12 AB3 ASP A 283 GLN A 301 1 19 HELIX 13 AB4 ILE A 315 LYS A 328 1 14 HELIX 14 AB5 ASP A 347 GLU A 364 1 18 HELIX 15 AB6 MET A 394 GLU A 399 1 6 HELIX 16 AB7 SER A 413 ASN A 423 1 11 HELIX 17 AB8 ASP A 436 LEU A 447 1 12 HELIX 18 AB9 PHE A 469 MET A 471 5 3 HELIX 19 AC1 LEU A 478 HIS A 484 1 7 SHEET 1 AA1 2 ILE A 23 ILE A 25 0 SHEET 2 AA1 2 GLU A 28 HIS A 30 -1 O HIS A 30 N ILE A 23 SHEET 1 AA2 2 LYS A 37 PHE A 41 0 SHEET 2 AA2 2 GLU A 48 GLU A 53 -1 O LEU A 49 N VAL A 40 SHEET 1 AA3 3 THR A 144 ILE A 145 0 SHEET 2 AA3 3 PHE A 151 PRO A 159 -1 O THR A 153 N ILE A 145 SHEET 3 AA3 3 THR A 487 LYS A 495 -1 O VAL A 494 N PHE A 152 SHEET 1 AA4 6 VAL A 219 ILE A 221 0 SHEET 2 AA4 6 THR A 189 LYS A 193 1 N VAL A 192 O ASN A 220 SHEET 3 AA4 6 VAL A 162 ILE A 166 1 N CYS A 163 O THR A 189 SHEET 4 AA4 6 LYS A 241 THR A 245 1 O ALA A 243 N ILE A 166 SHEET 5 AA4 6 ARG A 265 GLU A 269 1 O ARG A 265 N VAL A 242 SHEET 6 AA4 6 GLY A 473 ASN A 474 -1 O ASN A 474 N LEU A 268 SHEET 1 AA5 7 LYS A 367 CYS A 370 0 SHEET 2 AA5 7 THR A 385 SER A 388 -1 O VAL A 386 N GLU A 369 SHEET 3 AA5 7 VAL A 405 PHE A 411 1 O GLN A 406 N PHE A 387 SHEET 4 AA5 7 ARG A 308 GLU A 312 1 N VAL A 311 O MET A 409 SHEET 5 AA5 7 PRO A 275 VAL A 278 1 N VAL A 278 O PHE A 310 SHEET 6 AA5 7 SER A 429 PHE A 433 1 O PHE A 433 N ILE A 277 SHEET 7 AA5 7 THR A 451 VAL A 454 1 O TRP A 453 N VAL A 432 SHEET 1 AA6 2 PRO A 374 TRP A 375 0 SHEET 2 AA6 2 PHE A 381 VAL A 382 -1 O PHE A 381 N TRP A 375 LINK YB YB A 601 O HOH A 747 1555 1555 2.19 LINK YB YB A 601 O HOH A 819 1555 1555 3.11 LINK YB YB A 601 O HOH A 825 1555 1555 2.29 LINK YB YB A 601 O HOH A 838 1555 1555 2.19 LINK YB YB A 601 O HOH A 851 1555 1555 2.29 LINK YB YB A 601 O HOH A 858 1555 1555 2.28 LINK YB YB A 601 O HOH A 858 1555 8556 2.26 LINK YB YB A 601 O HOH A 866 1555 1555 2.32 LINK YB YB A 602 O2A NAI A 604 1555 1555 2.24 LINK YB YB A 602 O1N NAI A 604 1555 1555 2.23 LINK YB YB A 602 O HOH A 701 1555 1555 2.25 LINK YB YB A 602 O HOH A 780 1555 1555 2.23 LINK YB YB A 602 O HOH A 842 1555 1555 2.65 LINK YB YB A 602 O HOH A 859 1555 1555 2.16 SITE 1 AC1 7 HOH A 747 HOH A 815 HOH A 825 HOH A 838 SITE 2 AC1 7 HOH A 851 HOH A 858 HOH A 866 SITE 1 AC2 8 NAI A 604 CL A 605 CL A 610 CL A 611 SITE 2 AC2 8 HOH A 701 HOH A 780 HOH A 842 HOH A 859 SITE 1 AC3 11 GLY A 125 THR A 129 PHE A 171 MET A 175 SITE 2 AC3 11 TRP A 178 HIS A 293 TYR A 297 ILE A 304 SITE 3 AC3 11 TYR A 457 GLY A 458 VAL A 460 SITE 1 AC4 29 ILE A 166 ILE A 167 PRO A 168 TRP A 169 SITE 2 AC4 29 ASN A 170 LYS A 193 ALA A 195 GLU A 196 SITE 3 AC4 29 GLY A 226 PRO A 227 GLY A 230 ALA A 231 SITE 4 AC4 29 PHE A 244 THR A 245 GLY A 246 SER A 247 SITE 5 AC4 29 VAL A 250 GLU A 269 LEU A 270 CYS A 303 SITE 6 AC4 29 GLN A 350 LYS A 353 GLU A 400 PHE A 402 SITE 7 AC4 29 YB A 602 CL A 605 CL A 610 HOH A 701 SITE 8 AC4 29 HOH A 749 SITE 1 AC5 5 GLU A 349 YB A 602 NAI A 604 CL A 610 SITE 2 AC5 5 CL A 611 SITE 1 AC6 1 ASP A 283 SITE 1 AC7 1 HOH A 747 SITE 1 AC8 2 THR A 155 HIS A 157 SITE 1 AC9 6 GLU A 349 YB A 602 NAI A 604 CL A 605 SITE 2 AC9 6 CL A 611 HOH A 859 SITE 1 AD1 6 GLU A 349 YB A 602 CL A 605 CL A 610 SITE 2 AD1 6 HOH A 842 HOH A 859 CRYST1 108.802 108.802 82.877 90.00 90.00 90.00 P 4 2 2 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 0.009191 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009191 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012066 0.00000