HEADER CYTOSOLIC PROTEIN 26-AUG-20 7JWU TITLE CRYSTAL STRUCTURE OF HUMAN ALDH1A1 BOUND TO COMPOUND (R)-28 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 ENGINEERED: YES; COMPND 7 MUTATION: 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 BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET7B KEYWDS ROSSMANN FOLD, CYTOSOLIC PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.D.HURLEY,C.BUCHMAN REVDAT 2 18-OCT-23 7JWU 1 REMARK REVDAT 1 30-DEC-20 7JWU 0 JRNL AUTH B.C.HUDDLE,E.GRIMLEY,M.CHTCHERBININE,C.D.BUCHMAN, JRNL AUTH 2 C.TAKAHASHI,B.DEBNATH,S.C.MCGONIGAL,S.MAO,S.LI,J.FELTON, JRNL AUTH 3 S.PAN,B.WEN,D.SUN,N.NEAMATI,R.J.BUCKANOVICH,T.D.HURLEY, JRNL AUTH 4 S.D.LARSEN JRNL TITL DEVELOPMENT OF 2,5-DIHYDRO-4H-PYRAZOLO[3,4-D]PYRIMIDIN-4-ONE JRNL TITL 2 INHIBITORS OF ALDEHYDE DEHYDROGENASE 1A (ALDH1A) AS JRNL TITL 3 POTENTIAL ADJUNCTS TO OVARIAN CANCER CHEMOTHERAPY. JRNL REF EUR.J.MED.CHEM. V. 211 13060 2020 JRNL REFN ISSN 0223-5234 JRNL PMID 33341649 JRNL DOI 10.1016/J.EJMECH.2020.113060 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0155 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 109.03 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 36888 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) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1974 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2670 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.45 REMARK 3 BIN R VALUE (WORKING SET) : 0.3390 REMARK 3 BIN FREE R VALUE SET COUNT : 160 REMARK 3 BIN FREE R VALUE : 0.4030 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 : 74 REMARK 3 SOLVENT ATOMS : 289 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.31000 REMARK 3 B22 (A**2) : -2.31000 REMARK 3 B33 (A**2) : 4.62000 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): 0.183 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.173 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.185 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.127 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.935 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4003 ; 0.009 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3804 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5436 ; 1.368 ; 1.983 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8786 ; 0.901 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 501 ; 6.291 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 167 ;37.993 ;24.731 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 677 ;14.342 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;15.101 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 598 ; 0.073 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4521 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 894 ; 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 : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 8 A 140 REMARK 3 RESIDUE RANGE : A 163 A 269 REMARK 3 ORIGIN FOR THE GROUP (A): 54.091 -22.232 21.091 REMARK 3 T TENSOR REMARK 3 T11: 0.0816 T22: 0.0325 REMARK 3 T33: 0.5284 T12: 0.0210 REMARK 3 T13: 0.1090 T23: 0.0269 REMARK 3 L TENSOR REMARK 3 L11: 1.3286 L22: 0.8741 REMARK 3 L33: 1.2450 L12: 0.4297 REMARK 3 L13: -0.4393 L23: -0.3969 REMARK 3 S TENSOR REMARK 3 S11: -0.1252 S12: -0.1410 S13: -0.0928 REMARK 3 S21: 0.0944 S22: -0.0457 S23: 0.1430 REMARK 3 S31: 0.1633 S32: -0.0054 S33: 0.1709 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 270 A 485 REMARK 3 ORIGIN FOR THE GROUP (A): 28.213 -10.315 21.178 REMARK 3 T TENSOR REMARK 3 T11: 0.0599 T22: 0.0822 REMARK 3 T33: 0.5560 T12: 0.0235 REMARK 3 T13: 0.0832 T23: -0.0198 REMARK 3 L TENSOR REMARK 3 L11: 0.7941 L22: 1.5122 REMARK 3 L33: 1.3048 L12: 0.2726 REMARK 3 L13: -0.3259 L23: -0.9647 REMARK 3 S TENSOR REMARK 3 S11: -0.1286 S12: -0.0820 S13: -0.1205 REMARK 3 S21: 0.1480 S22: 0.1213 S23: 0.2651 REMARK 3 S31: 0.0125 S32: -0.1939 S33: 0.0073 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 141 A 162 REMARK 3 RESIDUE RANGE : A 486 A 501 REMARK 3 ORIGIN FOR THE GROUP (A): 69.211 3.140 4.893 REMARK 3 T TENSOR REMARK 3 T11: 0.0169 T22: 0.0149 REMARK 3 T33: 0.4596 T12: -0.0020 REMARK 3 T13: -0.0282 T23: 0.0420 REMARK 3 L TENSOR REMARK 3 L11: 0.3248 L22: 0.7949 REMARK 3 L33: 0.9954 L12: -0.4181 REMARK 3 L13: -0.1878 L23: -0.2336 REMARK 3 S TENSOR REMARK 3 S11: -0.0631 S12: -0.0289 S13: 0.0012 REMARK 3 S21: 0.1040 S22: 0.0042 S23: -0.0617 REMARK 3 S31: -0.0269 S32: 0.0642 S33: 0.0590 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 601 A 601 REMARK 3 ORIGIN FOR THE GROUP (A): 30.408 -29.682 39.655 REMARK 3 T TENSOR REMARK 3 T11: 0.1791 T22: 0.1599 REMARK 3 T33: 0.7044 T12: 0.0155 REMARK 3 T13: 0.1390 T23: 0.1301 REMARK 3 L TENSOR REMARK 3 L11: 0.0000 L22: 0.0000 REMARK 3 L33: 0.0000 L12: 0.0000 REMARK 3 L13: 0.0000 L23: 0.0000 REMARK 3 S TENSOR REMARK 3 S11: 0.0000 S12: 0.0000 S13: 0.0000 REMARK 3 S21: 0.0000 S22: 0.0000 S23: 0.0000 REMARK 3 S31: 0.0000 S32: 0.0000 S33: -0.0000 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK 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 7JWU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-AUG-20. REMARK 100 THE DEPOSITION ID IS D_1000251507. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-MAR-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-BM 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39319 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 109.030 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 9.500 REMARK 200 R MERGE (I) : 0.10600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.5 REMARK 200 DATA REDUNDANCY IN SHELL : 9.00 REMARK 200 R MERGE FOR SHELL (I) : 0.77600 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: REFMAC REMARK 200 STARTING MODEL: 6DUM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM SODIUM BISTRIS, PH 6.4, 9% REMARK 280 PEG3350, 200 MM NACL, AND 5-10 MM YBCL3, 250 UM 1-METHYL-5- REMARK 280 PHENYL-6-((1-(PYRIDIN-2-YL)ETHYL)THIO)-1,5-DIHYDRO-4H-PYRAZOLO[3, REMARK 280 4-D]PYRIMIDIN-4-ONE AND 1% V/V DMSO, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293K 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: 28230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 58050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -232.0 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 109.03200 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 109.03200 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 HOH A 979 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 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 O HOH A 788 O HOH A 788 5655 1.06 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 ASP A 99 35.08 -97.14 REMARK 500 SER A 121 -64.24 -102.06 REMARK 500 SER A 121 -64.24 -102.06 REMARK 500 THR A 228 -77.68 -102.85 REMARK 500 SER A 261 -84.17 -91.23 REMARK 500 LEU A 270 -157.15 -122.70 REMARK 500 GLN A 301 45.20 -97.61 REMARK 500 TYR A 380 56.58 -92.84 REMARK 500 LYS A 470 -139.33 55.55 REMARK 500 LEU A 478 178.16 67.98 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 720 O REMARK 620 2 HOH A 765 O 65.8 REMARK 620 3 HOH A 904 O 83.4 94.7 REMARK 620 4 HOH A 969 O 42.5 108.0 75.6 REMARK 620 5 HOH A 972 O 113.6 75.2 152.9 131.3 REMARK 620 6 HOH A 972 O 76.2 133.6 106.6 43.4 98.3 REMARK 620 7 HOH A 989 O 79.3 134.6 51.7 41.9 148.5 55.4 REMARK 620 N 1 2 3 4 5 6 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 NAD A 605 O2A REMARK 620 2 NAD A 605 O1N 70.1 REMARK 620 3 HOH A 706 O 158.3 89.1 REMARK 620 4 HOH A 729 O 107.3 74.7 59.1 REMARK 620 5 HOH A 772 O 73.6 77.4 108.9 149.6 REMARK 620 6 HOH A 961 O 83.9 119.4 101.6 62.1 145.5 REMARK 620 7 HOH A 973 O 124.4 165.4 76.4 98.6 105.5 66.2 REMARK 620 N 1 2 3 4 5 6 DBREF 7JWU A 1 501 UNP V9HW83 V9HW83_HUMAN 1 501 SEQADV 7JWU SER A 121 UNP V9HW83 ASN 121 ENGINEERED MUTATION 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 CL A 603 1 HET CL A 604 1 HET NAD A 605 44 HET VMA A 606 26 HETNAM YB YTTERBIUM (III) ION HETNAM CL CHLORIDE ION HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM VMA 1-METHYL-5-PHENYL-6-{[(1R)-1-(PYRIDIN-2-YL) HETNAM 2 VMA ETHYL]SULFANYL}-1,5-DIHYDRO-4H-PYRAZOLO[3,4- HETNAM 3 VMA D]PYRIMIDIN-4-ONE FORMUL 2 YB 2(YB 3+) FORMUL 4 CL 2(CL 1-) FORMUL 6 NAD C21 H27 N7 O14 P2 FORMUL 7 VMA C19 H17 N5 O S FORMUL 8 HOH *289(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 TYR A 297 1 15 HELIX 13 AB4 HIS A 298 GLN A 301 5 4 HELIX 14 AB5 ILE A 315 LYS A 328 1 14 HELIX 15 AB6 ASP A 347 GLU A 364 1 18 HELIX 16 AB7 MET A 394 GLU A 399 1 6 HELIX 17 AB8 SER A 413 ASN A 423 1 11 HELIX 18 AB9 ASP A 436 LEU A 447 1 12 HELIX 19 AC1 PHE A 469 MET A 471 5 3 HELIX 20 AC2 LEU A 478 GLU A 485 1 8 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 LYS A 241 N GLY A 164 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 ILE A 309 O MET A 409 SHEET 5 AA5 7 PRO A 275 VAL A 278 1 N CYS A 276 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 ALA A 430 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 720 1555 1555 2.43 LINK YB YB A 601 O HOH A 765 1555 1555 2.32 LINK YB YB A 601 O HOH A 904 1555 1555 2.71 LINK YB YB A 601 O HOH A 969 1555 1555 3.34 LINK YB YB A 601 O HOH A 972 1555 1555 2.88 LINK YB YB A 601 O HOH A 972 1555 8556 2.87 LINK YB YB A 601 O HOH A 989 1555 1555 2.69 LINK YB YB A 602 O2A NAD A 605 1555 1555 2.47 LINK YB YB A 602 O1N NAD A 605 1555 1555 2.21 LINK YB YB A 602 O HOH A 706 1555 1555 2.17 LINK YB YB A 602 O HOH A 729 1555 1555 2.80 LINK YB YB A 602 O HOH A 772 1555 1555 2.69 LINK YB YB A 602 O HOH A 961 1555 1555 2.74 LINK YB YB A 602 O HOH A 973 1555 1555 2.05 CRYST1 109.032 109.032 82.888 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 0.009172 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009172 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012064 0.00000