PDB Short entry for 4WDX HEADER OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR 09-SEP-14 4WDX TITLE 17BETA-HSD5 IN COMPLEX WITH [4-(2-HYDROXYETHYL)PIPERIDIN-1-YL](5- TITLE 2 METHYL-1H-INDOL-2-YL)METHANONE 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 REVDAT 3 14-DEC-22 4WDX 1 SOURCE KEYWDS REMARK SEQADV REVDAT 2 10-JUN-15 4WDX 1 JRNL REVDAT 1 15-APR-15 4WDX 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. 1.64 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 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) : 1.64 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.27 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 3 NUMBER OF REFLECTIONS : 72670 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) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3855 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) : 1.64 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.68 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5139 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.05 REMARK 3 BIN R VALUE (WORKING SET) : 0.4990 REMARK 3 BIN FREE R VALUE SET COUNT : 272 REMARK 3 BIN FREE R VALUE : 0.5020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4804 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 138 REMARK 3 SOLVENT ATOMS : 276 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.64 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : -0.01000 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): 0.115 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.113 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.079 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.346 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.945 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5056 ; 0.022 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6851 ; 2.253 ; 2.005 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 594 ; 6.316 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 225 ;37.009 ;23.867 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 888 ;15.039 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 34 ;21.422 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 754 ; 0.180 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3854 ; 0.013 ; 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): 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 : 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 4WDX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-SEP-14. REMARK 100 THE DEPOSITION ID IS D_1000203647. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JUL-08 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E+ SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS VII REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 76592 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.640 REMARK 200 RESOLUTION RANGE LOW (A) : 59.510 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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 (%): 43.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES, 0.2M AMMONIUM DIHYDROGEN REMARK 280 PHOSPHATE, 20-25% (W/V) PEG3350, PH 6.5, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 298K 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 38.61350 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1200 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL 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 GLN A 5 REMARK 465 GLU A 126 REMARK 465 GLU A 127 REMARK 465 ASP A 132 REMARK 465 GLU A 133 REMARK 465 ASN A 134 REMARK 465 GLY A 135 REMARK 465 LYS A 136 REMARK 465 VAL A 137 REMARK 465 ALA A 312 REMARK 465 SER A 313 REMARK 465 HIS A 314 REMARK 465 PRO A 315 REMARK 465 ASN A 316 REMARK 465 TYR A 317 REMARK 465 PRO A 318 REMARK 465 TYR A 319 REMARK 465 SER A 320 REMARK 465 ASP A 321 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 GLN B 5 REMARK 465 GLU B 126 REMARK 465 GLU B 127 REMARK 465 GLU B 133 REMARK 465 ASN B 134 REMARK 465 ALA B 312 REMARK 465 SER B 313 REMARK 465 HIS B 314 REMARK 465 PRO B 315 REMARK 465 ASN B 316 REMARK 465 TYR B 317 REMARK 465 PRO B 318 REMARK 465 TYR B 319 REMARK 465 SER B 320 REMARK 465 ASP B 321 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 C GLY B 125 O HOH B 612 1.98 REMARK 500 NH1 ARG A 31 O HOH A 622 2.00 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 ARG A 31 NE - CZ - NH1 ANGL. DEV. = -3.4 DEGREES REMARK 500 LEU A 63 CA - CB - CG ANGL. DEV. = 14.6 DEGREES REMARK 500 ARG A 66 NE - CZ - NH1 ANGL. DEV. = -9.4 DEGREES REMARK 500 ARG A 66 NE - CZ - NH2 ANGL. DEV. = 6.7 DEGREES REMARK 500 LEU A 103 CB - CG - CD2 ANGL. DEV. = 14.1 DEGREES REMARK 500 ARG A 171 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG A 250 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 250 NE - CZ - NH2 ANGL. DEV. = 4.9 DEGREES REMARK 500 ASP B 12 CB - CG - OD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 ARG B 31 NE - CZ - NH1 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG B 31 NE - CZ - NH2 ANGL. DEV. = 3.6 DEGREES REMARK 500 ASP B 112 CB - CG - OD1 ANGL. DEV. = -5.7 DEGREES REMARK 500 LEU B 177 CB - CG - CD1 ANGL. DEV. = -12.7 DEGREES REMARK 500 ARG B 226 CB - CA - C ANGL. DEV. = 14.5 DEGREES REMARK 500 ARG B 226 CA - CB - CG ANGL. DEV. = 14.6 DEGREES REMARK 500 ARG B 226 CG - CD - NE ANGL. DEV. = 20.2 DEGREES REMARK 500 ASP B 238 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 ARG B 250 NE - CZ - NH1 ANGL. DEV. = -4.0 DEGREES REMARK 500 ARG B 250 NE - CZ - NH2 ANGL. DEV. = 8.2 DEGREES REMARK 500 ARG B 278 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG B 278 NE - CZ - NH2 ANGL. DEV. = 4.8 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 ASP A 140 103.19 -167.88 REMARK 500 CYS A 193 116.91 -162.99 REMARK 500 PHE A 197 76.61 -159.44 REMARK 500 SER A 221 163.62 81.24 REMARK 500 ARG A 250 -144.69 -120.62 REMARK 500 ARG A 301 11.75 -146.03 REMARK 500 SER B 51 -166.65 -129.16 REMARK 500 ASP B 71 8.37 -69.58 REMARK 500 PHE B 197 76.95 -160.68 REMARK 500 SER B 221 164.43 85.48 REMARK 500 ARG B 250 -152.68 -126.71 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 WDX 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 WDX B 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4WDS RELATED DB: PDB REMARK 900 RELATED ID: 4WDT RELATED DB: PDB REMARK 900 RELATED ID: 4WDU RELATED DB: PDB REMARK 900 RELATED ID: 4WDV RELATED DB: PDB REMARK 900 RELATED ID: 4WDW RELATED DB: PDB DBREF 4WDX A 1 323 UNP P42330 AK1C3_HUMAN 1 323 DBREF 4WDX B 1 323 UNP P42330 AK1C3_HUMAN 1 323 SEQADV 4WDX GLN A 5 UNP P42330 HIS 5 VARIANT SEQADV 4WDX LEU A 324 UNP P42330 EXPRESSION TAG SEQADV 4WDX GLU A 325 UNP P42330 EXPRESSION TAG SEQADV 4WDX HIS A 326 UNP P42330 EXPRESSION TAG SEQADV 4WDX HIS A 327 UNP P42330 EXPRESSION TAG SEQADV 4WDX HIS A 328 UNP P42330 EXPRESSION TAG SEQADV 4WDX HIS A 329 UNP P42330 EXPRESSION TAG SEQADV 4WDX HIS A 330 UNP P42330 EXPRESSION TAG SEQADV 4WDX HIS A 331 UNP P42330 EXPRESSION TAG SEQADV 4WDX GLN B 5 UNP P42330 HIS 5 VARIANT SEQADV 4WDX LEU B 324 UNP P42330 EXPRESSION TAG SEQADV 4WDX GLU B 325 UNP P42330 EXPRESSION TAG SEQADV 4WDX HIS B 326 UNP P42330 EXPRESSION TAG SEQADV 4WDX HIS B 327 UNP P42330 EXPRESSION TAG SEQADV 4WDX HIS B 328 UNP P42330 EXPRESSION TAG SEQADV 4WDX HIS B 329 UNP P42330 EXPRESSION TAG SEQADV 4WDX HIS B 330 UNP P42330 EXPRESSION TAG SEQADV 4WDX HIS B 331 UNP P42330 EXPRESSION TAG SEQRES 1 A 331 MET ASP SER LYS GLN 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 GLN 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 WDX A 402 21 HET NAP B 401 48 HET WDX B 402 21 HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETNAM WDX [4-(2-HYDROXYETHYL)PIPERIDIN-1-YL](5-METHYL-1H-INDOL-2- HETNAM 2 WDX YL)METHANONE HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE FORMUL 3 NAP 2(C21 H28 N7 O17 P3) FORMUL 4 WDX 2(C17 H22 N2 O2) FORMUL 7 HOH *276(H2 O) HELIX 1 AA1 ARG A 31 GLY A 45 1 15 HELIX 2 AA2 ALA A 52 ASN A 56 5 5 HELIX 3 AA3 ASN A 57 ASP A 71 1 15 HELIX 4 AA4 LYS A 75 ILE A 79 5 5 HELIX 5 AA5 TRP A 86 HIS A 90 5 5 HELIX 6 AA6 ARG A 91 GLU A 93 5 3 HELIX 7 AA7 LEU A 94 GLN A 107 1 14 HELIX 8 AA8 ASP A 143 ALA A 157 1 15 HELIX 9 AA9 ASN A 169 ASN A 178 1 10 HELIX 10 AB1 ARG A 199 LYS A 209 1 11 HELIX 11 AB2 VAL A 234 GLU A 237 5 4 HELIX 12 AB3 ASP A 238 LYS A 249 1 12 HELIX 13 AB4 THR A 251 ARG A 263 1 13 HELIX 14 AB5 ASN A 273 VAL A 281 1 9 HELIX 15 AB6 GLN A 282 PHE A 286 5 5 HELIX 16 AB7 THR A 289 GLY A 298 1 10 HELIX 17 AB8 ASN A 307 PHE A 311 5 5 HELIX 18 AB9 SER B 32 GLY B 45 1 14 HELIX 19 AC1 ALA B 52 ASN B 56 5 5 HELIX 20 AC2 ASN B 57 ASP B 71 1 15 HELIX 21 AC3 LYS B 75 ILE B 79 5 5 HELIX 22 AC4 TRP B 86 HIS B 90 5 5 HELIX 23 AC5 ARG B 91 GLU B 93 5 3 HELIX 24 AC6 LEU B 94 GLN B 107 1 14 HELIX 25 AC7 ASP B 143 ALA B 157 1 15 HELIX 26 AC8 ASN B 169 ASN B 178 1 10 HELIX 27 AC9 ARG B 199 LYS B 209 1 11 HELIX 28 AD1 VAL B 234 GLU B 237 5 4 HELIX 29 AD2 ASP B 238 LYS B 249 1 12 HELIX 30 AD3 THR B 251 ARG B 263 1 13 HELIX 31 AD4 ASN B 273 VAL B 281 1 9 HELIX 32 AD5 GLN B 282 PHE B 286 5 5 HELIX 33 AD6 THR B 289 GLY B 298 1 10 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 ASP A 50 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 GLN A 190 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 20 O VAL A 267 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 ASP B 50 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 CYS B 188 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 20 O VAL B 267 SITE 1 AC1 31 GLY A 22 THR A 23 TYR A 24 ASP A 50 SITE 2 AC1 31 TYR A 55 HIS A 117 SER A 166 ASN A 167 SITE 3 AC1 31 GLN A 190 TYR A 216 SER A 217 ALA A 218 SITE 4 AC1 31 LEU A 219 GLY A 220 SER A 221 GLN A 222 SITE 5 AC1 31 ALA A 253 LEU A 268 ALA A 269 LYS A 270 SITE 6 AC1 31 SER A 271 TYR A 272 ARG A 276 GLN A 279 SITE 7 AC1 31 ASN A 280 WDX A 402 HOH A 536 HOH A 560 SITE 8 AC1 31 HOH A 564 HOH A 591 HOH A 592 SITE 1 AC2 13 TYR A 24 LEU A 54 TYR A 55 TRP A 86 SITE 2 AC2 13 HIS A 117 SER A 118 ASN A 167 GLN A 222 SITE 3 AC2 13 TRP A 227 PHE A 306 PHE A 311 NAP A 401 SITE 4 AC2 13 HOH A 574 SITE 1 AC3 31 GLY B 22 THR B 23 TYR B 24 ASP B 50 SITE 2 AC3 31 TYR B 55 HIS B 117 SER B 166 ASN B 167 SITE 3 AC3 31 GLN B 190 TYR B 216 SER B 217 ALA B 218 SITE 4 AC3 31 LEU B 219 GLY B 220 SER B 221 GLN B 222 SITE 5 AC3 31 LEU B 236 ALA B 253 LEU B 268 ALA B 269 SITE 6 AC3 31 LYS B 270 SER B 271 TYR B 272 ARG B 276 SITE 7 AC3 31 GLN B 279 ASN B 280 WDX B 402 HOH B 536 SITE 8 AC3 31 HOH B 578 HOH B 582 HOH B 587 SITE 1 AC4 15 TYR B 24 LEU B 54 TYR B 55 TRP B 86 SITE 2 AC4 15 HIS B 117 SER B 118 MET B 120 ASN B 167 SITE 3 AC4 15 SER B 221 GLN B 222 TRP B 227 PHE B 306 SITE 4 AC4 15 PHE B 311 NAP B 401 HOH B 543 CRYST1 60.041 77.227 72.208 90.00 97.62 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 0.016655 0.000000 0.002227 0.00000 SCALE2 0.000000 0.012949 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013972 0.00000