HEADER OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR 27-JAN-15 4XVD TITLE 17BETA-HSD5 IN COMPLEX WITH 4-NITRO-2-({4-[3-(TRIFLUOROMETHYL) TITLE 2 PHENYL]PIPERAZIN-1-YL}METHYL)PHENOL COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALDO-KETO REDUCTASE FAMILY 1 MEMBER C3; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: 17-BETA-HYDROXYSTEROID DEHYDROGENASE TYPE 5,17-BETA-HSD 5, COMPND 5 TESTOSTERONE 17-BETA-DEHYDROGENASE 5; COMPND 6 EC: 1.1.1.64; 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: AKR1C3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ALDO-KETO REDUCTASE INHIBITOR, OXIDOREDUCTASE-OXIDOREDUCTASE KEYWDS 2 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.AMANO,T.YAMAGUCHI,T.NIIMI,H.SAKASHITA REVDAT 4 08-NOV-23 4XVD 1 REMARK REVDAT 3 05-FEB-20 4XVD 1 SOURCE REMARK REVDAT 2 10-JUN-15 4XVD 1 JRNL REVDAT 1 15-APR-15 4XVD 0 JRNL AUTH Y.AMANO,T.YAMAGUCHI,T.NIIMI,H.SAKASHITA JRNL TITL STRUCTURES OF COMPLEXES OF TYPE 5 17 BETA-HYDROXYSTEROID JRNL TITL 2 DEHYDROGENASE WITH STRUCTURALLY DIVERSE INHIBITORS: INSIGHTS JRNL TITL 3 INTO THE CONFORMATIONAL CHANGES UPON INHIBITOR BINDING. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 71 918 2015 JRNL REFN ESSN 1399-0047 JRNL PMID 25849402 JRNL DOI 10.1107/S1399004715002175 REMARK 2 REMARK 2 RESOLUTION. 2.81 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 : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.81 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.67 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 90.4 REMARK 3 NUMBER OF REFLECTIONS : 16372 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) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 894 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) : 2.81 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.89 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1202 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.01 REMARK 3 BIN R VALUE (WORKING SET) : 0.3130 REMARK 3 BIN FREE R VALUE SET COUNT : 59 REMARK 3 BIN FREE R VALUE : 0.3240 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5010 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 150 REMARK 3 SOLVENT ATOMS : 13 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.59 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.03000 REMARK 3 B22 (A**2) : 0.03000 REMARK 3 B33 (A**2) : -0.06000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.431 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.331 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 17.076 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.910 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.854 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5282 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7165 ; 1.628 ; 2.005 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 618 ; 5.894 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 239 ;37.334 ;24.017 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 915 ;19.575 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 34 ;19.684 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 781 ; 0.093 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4076 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 2493 ; 2.029 ; 3.298 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3104 ; 3.372 ; 4.932 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2789 ; 2.188 ; 3.396 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): 8197 ; 6.192 ;27.815 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 : 3 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 6 A 321 1 REMARK 3 1 B 6 B 321 1 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT THERMAL 1 A (A**2): 2478 ;11.780 ; 0.500 REMARK 3 REMARK 3 NCS GROUP NUMBER : 2 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 401 A 401 1 REMARK 3 1 B 401 B 401 1 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT THERMAL 2 A (A**2): 48 ;16.000 ; 0.500 REMARK 3 REMARK 3 NCS GROUP NUMBER : 3 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 402 A 402 1 REMARK 3 1 B 402 B 402 1 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT THERMAL 3 A (A**2): 27 ;10.740 ; 0.500 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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: NULL REMARK 4 REMARK 4 4XVD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-FEB-15. REMARK 100 THE DEPOSITION ID IS D_1000206365. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-DEC-05 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17267 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 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 (%) : 90.4 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : NULL 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) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.45400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 1S1P REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CITRATE, 0.4 M AMMONIUM REMARK 280 ACETATE, 2.5% (V/V) 2-METHYL-2,4-PENTANEDIOL, 22-30% (W/V) REMARK 280 PEG4000, PH 5.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 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+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 8555 Y+1/2,-X+1/2,Z+1/2 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 72.89750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 72.89750 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 37.14350 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 72.89750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 72.89750 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 37.14350 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 72.89750 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 72.89750 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 37.14350 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 72.89750 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 72.89750 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 37.14350 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 MET A 1 REMARK 465 ASP A 2 REMARK 465 SER A 3 REMARK 465 LYS A 4 REMARK 465 HIS A 5 REMARK 465 GLY A 125 REMARK 465 GLU A 126 REMARK 465 GLU A 322 REMARK 465 TYR A 323 REMARK 465 LEU A 324 REMARK 465 GLU A 325 REMARK 465 HIS A 326 REMARK 465 HIS A 327 REMARK 465 HIS A 328 REMARK 465 HIS A 329 REMARK 465 HIS A 330 REMARK 465 HIS A 331 REMARK 465 MET B 1 REMARK 465 ASP B 2 REMARK 465 SER B 3 REMARK 465 LYS B 4 REMARK 465 HIS B 5 REMARK 465 GLY B 72 REMARK 465 GLU B 133 REMARK 465 TYR B 272 REMARK 465 ASN B 273 REMARK 465 ASP B 309 REMARK 465 GLU B 322 REMARK 465 TYR B 323 REMARK 465 LEU B 324 REMARK 465 GLU B 325 REMARK 465 HIS B 326 REMARK 465 HIS B 327 REMARK 465 HIS B 328 REMARK 465 HIS B 329 REMARK 465 HIS B 330 REMARK 465 HIS B 331 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 NH1 ARG B 223 O SER B 232 1.99 REMARK 500 OG SER A 271 O3X NAP A 401 2.14 REMARK 500 NH2 ARG B 76 CE1 TYR B 110 2.14 REMARK 500 NH2 ARG B 76 OH TYR B 110 2.17 REMARK 500 NH2 ARG B 76 CZ TYR B 110 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLN B 6 CA GLN B 6 CB -0.135 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 GLN B 6 N - CA - CB ANGL. DEV. = -12.2 DEGREES REMARK 500 GLN B 6 CA - CB - CG ANGL. DEV. = -15.3 DEGREES REMARK 500 ARG B 223 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES 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 ASN A 11 3.50 -59.17 REMARK 500 ASN A 57 13.70 -145.70 REMARK 500 SER A 221 175.49 79.83 REMARK 500 ARG A 250 -168.78 -124.18 REMARK 500 ARG A 301 29.78 -144.09 REMARK 500 ASP B 156 -17.61 -43.69 REMARK 500 ASN B 167 18.79 59.04 REMARK 500 SER B 221 -178.93 71.54 REMARK 500 ARG B 223 45.35 73.60 REMARK 500 LEU B 236 7.96 -64.66 REMARK 500 ARG B 250 -162.85 -117.48 REMARK 500 ARG B 301 19.81 -143.54 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAP A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue WDV A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAP B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue WDV B 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4WDT RELATED DB: PDB REMARK 900 RELATED ID: 4WDU RELATED DB: PDB REMARK 900 RELATED ID: 4WDW RELATED DB: PDB REMARK 900 RELATED ID: 4WDX RELATED DB: PDB REMARK 900 RELATED ID: 4XVE RELATED DB: PDB DBREF 4XVD A 1 323 UNP P42330 AK1C3_HUMAN 1 323 DBREF 4XVD B 1 323 UNP P42330 AK1C3_HUMAN 1 323 SEQADV 4XVD LEU A 324 UNP P42330 EXPRESSION TAG SEQADV 4XVD GLU A 325 UNP P42330 EXPRESSION TAG SEQADV 4XVD HIS A 326 UNP P42330 EXPRESSION TAG SEQADV 4XVD HIS A 327 UNP P42330 EXPRESSION TAG SEQADV 4XVD HIS A 328 UNP P42330 EXPRESSION TAG SEQADV 4XVD HIS A 329 UNP P42330 EXPRESSION TAG SEQADV 4XVD HIS A 330 UNP P42330 EXPRESSION TAG SEQADV 4XVD HIS A 331 UNP P42330 EXPRESSION TAG SEQADV 4XVD LEU B 324 UNP P42330 EXPRESSION TAG SEQADV 4XVD GLU B 325 UNP P42330 EXPRESSION TAG SEQADV 4XVD HIS B 326 UNP P42330 EXPRESSION TAG SEQADV 4XVD HIS B 327 UNP P42330 EXPRESSION TAG SEQADV 4XVD HIS B 328 UNP P42330 EXPRESSION TAG SEQADV 4XVD HIS B 329 UNP P42330 EXPRESSION TAG SEQADV 4XVD HIS B 330 UNP P42330 EXPRESSION TAG SEQADV 4XVD HIS B 331 UNP P42330 EXPRESSION TAG SEQRES 1 A 331 MET ASP SER LYS HIS GLN CYS VAL LYS LEU ASN ASP GLY SEQRES 2 A 331 HIS PHE MET PRO VAL LEU GLY PHE GLY THR TYR ALA PRO SEQRES 3 A 331 PRO GLU VAL PRO ARG SER LYS ALA LEU GLU VAL THR LYS SEQRES 4 A 331 LEU ALA ILE GLU ALA GLY PHE ARG HIS ILE ASP SER ALA SEQRES 5 A 331 HIS LEU TYR ASN ASN GLU GLU GLN VAL GLY LEU ALA ILE SEQRES 6 A 331 ARG SER LYS ILE ALA ASP GLY SER VAL LYS ARG GLU ASP SEQRES 7 A 331 ILE PHE TYR THR SER LYS LEU TRP SER THR PHE HIS ARG SEQRES 8 A 331 PRO GLU LEU VAL ARG PRO ALA LEU GLU ASN SER LEU LYS SEQRES 9 A 331 LYS ALA GLN LEU ASP TYR VAL ASP LEU TYR LEU ILE HIS SEQRES 10 A 331 SER PRO MET SER LEU LYS PRO GLY GLU GLU LEU SER PRO SEQRES 11 A 331 THR ASP GLU ASN GLY LYS VAL ILE PHE ASP ILE VAL ASP SEQRES 12 A 331 LEU CYS THR THR TRP GLU ALA MET GLU LYS CYS LYS ASP SEQRES 13 A 331 ALA GLY LEU ALA LYS SER ILE GLY VAL SER ASN PHE ASN SEQRES 14 A 331 ARG ARG GLN LEU GLU MET ILE LEU ASN LYS PRO GLY LEU SEQRES 15 A 331 LYS TYR LYS PRO VAL CYS ASN GLN VAL GLU CYS HIS PRO SEQRES 16 A 331 TYR PHE ASN ARG SER LYS LEU LEU ASP PHE CYS LYS SER SEQRES 17 A 331 LYS ASP ILE VAL LEU VAL ALA TYR SER ALA LEU GLY SER SEQRES 18 A 331 GLN ARG ASP LYS ARG TRP VAL ASP PRO ASN SER PRO VAL SEQRES 19 A 331 LEU LEU GLU ASP PRO VAL LEU CYS ALA LEU ALA LYS LYS SEQRES 20 A 331 HIS LYS ARG THR PRO ALA LEU ILE ALA LEU ARG TYR GLN SEQRES 21 A 331 LEU GLN ARG GLY VAL VAL VAL LEU ALA LYS SER TYR ASN SEQRES 22 A 331 GLU GLN ARG ILE ARG GLN ASN VAL GLN VAL PHE GLU PHE SEQRES 23 A 331 GLN LEU THR ALA GLU ASP MET LYS ALA ILE ASP GLY LEU SEQRES 24 A 331 ASP ARG ASN LEU HIS TYR PHE ASN SER ASP SER PHE ALA SEQRES 25 A 331 SER HIS PRO ASN TYR PRO TYR SER ASP GLU TYR LEU GLU SEQRES 26 A 331 HIS HIS HIS HIS HIS HIS SEQRES 1 B 331 MET ASP SER LYS HIS GLN CYS VAL LYS LEU ASN ASP GLY SEQRES 2 B 331 HIS PHE MET PRO VAL LEU GLY PHE GLY THR TYR ALA PRO SEQRES 3 B 331 PRO GLU VAL PRO ARG SER LYS ALA LEU GLU VAL THR LYS SEQRES 4 B 331 LEU ALA ILE GLU ALA GLY PHE ARG HIS ILE ASP SER ALA SEQRES 5 B 331 HIS LEU TYR ASN ASN GLU GLU GLN VAL GLY LEU ALA ILE SEQRES 6 B 331 ARG SER LYS ILE ALA ASP GLY SER VAL LYS ARG GLU ASP SEQRES 7 B 331 ILE PHE TYR THR SER LYS LEU TRP SER THR PHE HIS ARG SEQRES 8 B 331 PRO GLU LEU VAL ARG PRO ALA LEU GLU ASN SER LEU LYS SEQRES 9 B 331 LYS ALA GLN LEU ASP TYR VAL ASP LEU TYR LEU ILE HIS SEQRES 10 B 331 SER PRO MET SER LEU LYS PRO GLY GLU GLU LEU SER PRO SEQRES 11 B 331 THR ASP GLU ASN GLY LYS VAL ILE PHE ASP ILE VAL ASP SEQRES 12 B 331 LEU CYS THR THR TRP GLU ALA MET GLU LYS CYS LYS ASP SEQRES 13 B 331 ALA GLY LEU ALA LYS SER ILE GLY VAL SER ASN PHE ASN SEQRES 14 B 331 ARG ARG GLN LEU GLU MET ILE LEU ASN LYS PRO GLY LEU SEQRES 15 B 331 LYS TYR LYS PRO VAL CYS ASN GLN VAL GLU CYS HIS PRO SEQRES 16 B 331 TYR PHE ASN ARG SER LYS LEU LEU ASP PHE CYS LYS SER SEQRES 17 B 331 LYS ASP ILE VAL LEU VAL ALA TYR SER ALA LEU GLY SER SEQRES 18 B 331 GLN ARG ASP LYS ARG TRP VAL ASP PRO ASN SER PRO VAL SEQRES 19 B 331 LEU LEU GLU ASP PRO VAL LEU CYS ALA LEU ALA LYS LYS SEQRES 20 B 331 HIS LYS ARG THR PRO ALA LEU ILE ALA LEU ARG TYR GLN SEQRES 21 B 331 LEU GLN ARG GLY VAL VAL VAL LEU ALA LYS SER TYR ASN SEQRES 22 B 331 GLU GLN ARG ILE ARG GLN ASN VAL GLN VAL PHE GLU PHE SEQRES 23 B 331 GLN LEU THR ALA GLU ASP MET LYS ALA ILE ASP GLY LEU SEQRES 24 B 331 ASP ARG ASN LEU HIS TYR PHE ASN SER ASP SER PHE ALA SEQRES 25 B 331 SER HIS PRO ASN TYR PRO TYR SER ASP GLU TYR LEU GLU SEQRES 26 B 331 HIS HIS HIS HIS HIS HIS HET NAP A 401 48 HET WDV A 402 27 HET NAP B 401 48 HET WDV B 402 27 HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETNAM WDV 4-NITRO-2-({4-[3-(TRIFLUOROMETHYL)PHENYL]PIPERAZIN-1- HETNAM 2 WDV YL}METHYL)PHENOL HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE FORMUL 3 NAP 2(C21 H28 N7 O17 P3) FORMUL 4 WDV 2(C18 H18 F3 N3 O3) FORMUL 7 HOH *13(H2 O) HELIX 1 AA1 PRO A 30 GLY A 45 1 16 HELIX 2 AA2 ASN A 57 ASP A 71 1 15 HELIX 3 AA3 LYS A 75 ILE A 79 5 5 HELIX 4 AA4 TRP A 86 HIS A 90 5 5 HELIX 5 AA5 ARG A 91 ALA A 106 1 16 HELIX 6 AA6 ASP A 143 ALA A 157 1 15 HELIX 7 AA7 ASN A 169 ASN A 178 1 10 HELIX 8 AA8 ARG A 199 LYS A 209 1 11 HELIX 9 AA9 VAL A 234 GLU A 237 5 4 HELIX 10 AB1 ASP A 238 HIS A 248 1 11 HELIX 11 AB2 THR A 251 GLN A 262 1 12 HELIX 12 AB3 ASN A 273 ASN A 280 1 8 HELIX 13 AB4 VAL A 281 GLU A 285 5 5 HELIX 14 AB5 THR A 289 GLY A 298 1 10 HELIX 15 AB6 SER A 310 HIS A 314 5 5 HELIX 16 AB7 PRO B 30 ALA B 44 1 15 HELIX 17 AB8 ASN B 57 ALA B 70 1 14 HELIX 18 AB9 TRP B 86 HIS B 90 5 5 HELIX 19 AC1 ARG B 91 ALA B 106 1 16 HELIX 20 AC2 ASP B 143 ASP B 156 1 14 HELIX 21 AC3 ASN B 169 ASN B 178 1 10 HELIX 22 AC4 ARG B 199 LYS B 209 1 11 HELIX 23 AC5 ASP B 238 LYS B 249 1 12 HELIX 24 AC6 THR B 251 GLN B 262 1 12 HELIX 25 AC7 GLN B 275 ASN B 280 1 6 HELIX 26 AC8 VAL B 281 GLU B 285 5 5 HELIX 27 AC9 THR B 289 GLY B 298 1 10 HELIX 28 AD1 SER B 308 SER B 308 5 1 HELIX 29 AD2 SER B 310 HIS B 314 5 5 SHEET 1 AA1 2 CYS A 7 LYS A 9 0 SHEET 2 AA1 2 PHE A 15 PRO A 17 -1 O MET A 16 N VAL A 8 SHEET 1 AA2 9 LEU A 19 GLY A 22 0 SHEET 2 AA2 9 HIS A 48 ASP A 50 1 O HIS A 48 N PHE A 21 SHEET 3 AA2 9 PHE A 80 LEU A 85 1 O PHE A 80 N ILE A 49 SHEET 4 AA2 9 VAL A 111 ILE A 116 1 O LEU A 115 N LEU A 85 SHEET 5 AA2 9 ALA A 160 SER A 166 1 O LYS A 161 N VAL A 111 SHEET 6 AA2 9 CYS A 188 GLU A 192 1 O CYS A 188 N VAL A 165 SHEET 7 AA2 9 VAL A 212 TYR A 216 1 O TYR A 216 N VAL A 191 SHEET 8 AA2 9 VAL A 266 LYS A 270 1 O VAL A 266 N ALA A 215 SHEET 9 AA2 9 LEU A 19 GLY A 22 1 N GLY A 22 O ALA A 269 SHEET 1 AA3 2 CYS B 7 LYS B 9 0 SHEET 2 AA3 2 PHE B 15 PRO B 17 -1 O MET B 16 N VAL B 8 SHEET 1 AA4 9 LEU B 19 GLY B 22 0 SHEET 2 AA4 9 HIS B 48 ASP B 50 1 O HIS B 48 N PHE B 21 SHEET 3 AA4 9 PHE B 80 LEU B 85 1 O PHE B 80 N ILE B 49 SHEET 4 AA4 9 VAL B 111 ILE B 116 1 O LEU B 115 N LEU B 85 SHEET 5 AA4 9 ALA B 160 SER B 166 1 O LYS B 161 N VAL B 111 SHEET 6 AA4 9 CYS B 188 GLU B 192 1 O GLN B 190 N VAL B 165 SHEET 7 AA4 9 VAL B 212 TYR B 216 1 O TYR B 216 N VAL B 191 SHEET 8 AA4 9 VAL B 266 LYS B 270 1 O VAL B 266 N ALA B 215 SHEET 9 AA4 9 LEU B 19 GLY B 22 1 N GLY B 22 O ALA B 269 SITE 1 AC1 27 GLY A 22 THR A 23 TYR A 24 ASP A 50 SITE 2 AC1 27 TYR A 55 LYS A 84 HIS A 117 SER A 166 SITE 3 AC1 27 ASN A 167 GLN A 190 TYR A 216 SER A 217 SITE 4 AC1 27 LEU A 219 GLY A 220 SER A 221 GLN A 222 SITE 5 AC1 27 LEU A 236 ALA A 253 LYS A 270 SER A 271 SITE 6 AC1 27 TYR A 272 ARG A 276 GLN A 279 ASN A 280 SITE 7 AC1 27 WDV A 402 HOH A 507 HOH A 510 SITE 1 AC2 15 TYR A 24 LEU A 54 TYR A 55 HIS A 117 SITE 2 AC2 15 ASN A 167 ASP A 224 TRP A 227 PHE A 306 SITE 3 AC2 15 ASN A 307 SER A 308 PHE A 311 TYR A 317 SITE 4 AC2 15 TYR A 319 NAP A 401 HOH A 507 SITE 1 AC3 24 GLY B 22 THR B 23 TYR B 24 ASP B 50 SITE 2 AC3 24 TYR B 55 HIS B 117 SER B 166 ASN B 167 SITE 3 AC3 24 GLN B 190 TYR B 216 SER B 217 LEU B 219 SITE 4 AC3 24 SER B 221 GLN B 222 LEU B 236 ALA B 253 SITE 5 AC3 24 LEU B 268 ALA B 269 LYS B 270 SER B 271 SITE 6 AC3 24 ARG B 276 GLN B 279 ASN B 280 WDV B 402 SITE 1 AC4 12 TYR B 24 LEU B 54 TYR B 55 HIS B 117 SITE 2 AC4 12 ASN B 167 TRP B 227 PHE B 306 ASN B 307 SITE 3 AC4 12 SER B 308 TYR B 317 TYR B 319 NAP B 401 CRYST1 145.795 145.795 74.287 90.00 90.00 90.00 I 4 16 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 0.006859 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006859 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013461 0.00000 MTRIX1 1 1.000000 0.000000 0.000000 0.00000 1 MTRIX2 1 0.000000 1.000000 0.000000 0.00000 1 MTRIX3 1 0.000000 0.000000 1.000000 0.00000 1 MTRIX1 2 -0.855833 0.512671 -0.068693 277.48206 1 MTRIX2 2 0.514401 0.857501 -0.009108 -75.76650 1 MTRIX3 2 0.054235 -0.043131 -0.997596 105.25424 1