HEADER OXIDOREDUCTASE 10-JUL-19 6KG2 TITLE HUMAN MTHFD2 IN COMPLEX WITH COMPOUND 18 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BIFUNCTIONAL METHYLENETETRAHYDROFOLATE COMPND 3 DEHYDROGENASE/CYCLOHYDROLASE, MITOCHONDRIAL; COMPND 4 CHAIN: A, B; COMPND 5 EC: 1.5.1.15,3.5.4.9; COMPND 6 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: MTHFD2, NMDMC; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS INHIBITOR, FOLATE, COFACTOR, DEHYDROGENASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR M.SUZUKI,Y.MATSUI,M.OTA,J.KAWAI REVDAT 3 27-MAR-24 6KG2 1 REMARK REVDAT 2 11-DEC-19 6KG2 1 JRNL REVDAT 1 13-NOV-19 6KG2 0 JRNL AUTH J.KAWAI,T.TOKI,M.OTA,H.INOUE,Y.TAKATA,T.ASAHI,M.SUZUKI, JRNL AUTH 2 T.SHIMADA,K.ONO,K.SUZUKI,S.TAKAISHI,H.OHKI,S.MATSUI, JRNL AUTH 3 S.TSUTSUMI,Y.HIROTA,K.NAKAYAMA JRNL TITL DISCOVERY OF A POTENT, SELECTIVE, AND ORALLY AVAILABLE JRNL TITL 2 MTHFD2 INHIBITOR (DS18561882) WITH IN VIVO ANTITUMOR JRNL TITL 3 ACTIVITY. JRNL REF J.MED.CHEM. V. 62 10204 2019 JRNL REFN ISSN 0022-2623 JRNL PMID 31638799 JRNL DOI 10.1021/ACS.JMEDCHEM.9B01113 REMARK 2 REMARK 2 RESOLUTION. 2.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0238 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) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 39354 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) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2134 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 15 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.25 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.33 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3805 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.77 REMARK 3 BIN R VALUE (WORKING SET) : 0.3390 REMARK 3 BIN FREE R VALUE SET COUNT : 182 REMARK 3 BIN FREE R VALUE : 0.3580 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4318 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 172 REMARK 3 SOLVENT ATOMS : 103 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 59.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.51000 REMARK 3 B22 (A**2) : 1.51000 REMARK 3 B33 (A**2) : -4.91000 REMARK 3 B12 (A**2) : 0.76000 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): 0.207 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.196 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.204 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.460 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4584 ; 0.007 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6270 ; 1.677 ; 1.659 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 579 ; 6.777 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 185 ;36.537 ;23.297 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 738 ;17.854 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;21.048 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 638 ; 0.105 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3362 ; 0.007 ; 0.020 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 : 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: U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6KG2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-JUL-19. REMARK 100 THE DEPOSITION ID IS D_1300012918. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-NOV-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A 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 : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41534 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250 REMARK 200 RESOLUTION RANGE LOW (A) : 46.220 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.04200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.31 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.64300 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 28% I-PROH, 0.1M BIS-TRIS, PH 6.5, 3% REMARK 280 PEG 200, 10 MM SPERMIDINE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 75.24600 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 37.62300 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 56.43450 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 18.81150 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 94.05750 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -50.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 16 REMARK 465 GLY A 17 REMARK 465 SER A 18 REMARK 465 SER A 19 REMARK 465 HIS A 20 REMARK 465 HIS A 21 REMARK 465 HIS A 22 REMARK 465 HIS A 23 REMARK 465 HIS A 24 REMARK 465 HIS A 25 REMARK 465 SER A 26 REMARK 465 SER A 27 REMARK 465 GLY A 28 REMARK 465 GLU A 29 REMARK 465 ASN A 30 REMARK 465 LEU A 31 REMARK 465 TYR A 32 REMARK 465 PHE A 33 REMARK 465 GLN A 34 REMARK 465 GLY A 35 REMARK 465 ASP A 281 REMARK 465 PRO A 282 REMARK 465 VAL A 283 REMARK 465 THR A 284 REMARK 465 ALA A 285 REMARK 465 LEU A 334 REMARK 465 GLU A 335 REMARK 465 GLU A 336 REMARK 465 ARG A 337 REMARK 465 GLU A 338 REMARK 465 MET B 16 REMARK 465 GLY B 17 REMARK 465 SER B 18 REMARK 465 SER B 19 REMARK 465 HIS B 20 REMARK 465 HIS B 21 REMARK 465 HIS B 22 REMARK 465 HIS B 23 REMARK 465 HIS B 24 REMARK 465 HIS B 25 REMARK 465 SER B 26 REMARK 465 SER B 27 REMARK 465 GLY B 28 REMARK 465 GLU B 29 REMARK 465 ASN B 30 REMARK 465 LEU B 31 REMARK 465 TYR B 32 REMARK 465 PHE B 33 REMARK 465 GLN B 34 REMARK 465 GLY B 35 REMARK 465 HIS B 280 REMARK 465 ASP B 281 REMARK 465 PRO B 282 REMARK 465 VAL B 283 REMARK 465 THR B 284 REMARK 465 ALA B 285 REMARK 465 LYS B 286 REMARK 465 ARG B 333 REMARK 465 LEU B 334 REMARK 465 GLU B 335 REMARK 465 GLU B 336 REMARK 465 ARG B 337 REMARK 465 GLU B 338 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 58 CG CD OE1 OE2 REMARK 470 MET A 103 CE REMARK 470 GLU A 111 CD OE1 OE2 REMARK 470 LYS A 119 CG CD CE NZ REMARK 470 LYS A 194 NZ REMARK 470 ILE A 230 CD1 REMARK 470 LYS A 237 CG CD CE NZ REMARK 470 GLU A 238 CG CD OE1 OE2 REMARK 470 LYS A 241 CE NZ REMARK 470 LYS A 242 CE NZ REMARK 470 ILE A 245 CG1 CG2 CD1 REMARK 470 GLU A 267 CG CD OE1 OE2 REMARK 470 ARG A 278 CD NE CZ NH1 NH2 REMARK 470 VAL A 279 CG1 CG2 REMARK 470 LYS A 286 CG CD CE NZ REMARK 470 LYS A 301 CE NZ REMARK 470 LEU A 332 CG CD1 CD2 REMARK 470 ARG A 333 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 119 CG CD CE NZ REMARK 470 ARG B 143 CG CD NE CZ NH1 NH2 REMARK 470 ILE B 230 CD1 REMARK 470 LYS B 237 CD CE NZ REMARK 470 GLU B 238 CG CD OE1 OE2 REMARK 470 LYS B 242 CE NZ REMARK 470 ILE B 245 CD1 REMARK 470 GLU B 267 CG CD OE1 OE2 REMARK 470 ARG B 278 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 296 CG CD OE1 OE2 REMARK 470 ARG B 299 CG CD NE CZ NH1 NH2 REMARK 470 GLN B 300 CG CD OE1 NE2 REMARK 470 LYS B 301 CG CD CE NZ REMARK 470 VAL B 331 CG1 CG2 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 ASN A 118 ND2 ASN A 122 2.13 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 TYR A 304 CB - CA - C ANGL. DEV. = -12.2 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 GLU A 77 30.76 -143.11 REMARK 500 THR A 191 -35.00 -131.55 REMARK 500 ARG A 201 25.24 -151.71 REMARK 500 VAL A 205 -64.81 -138.78 REMARK 500 HIS A 232 -167.91 -161.56 REMARK 500 LYS A 288 -158.22 -118.86 REMARK 500 PRO A 309 -176.95 -68.00 REMARK 500 LYS A 330 39.00 38.26 REMARK 500 LEU A 332 54.92 -103.40 REMARK 500 GLU B 77 25.76 -142.81 REMARK 500 ALA B 106 -29.90 -37.85 REMARK 500 THR B 191 -35.51 -130.86 REMARK 500 ARG B 201 21.87 -149.94 REMARK 500 VAL B 205 -69.75 -132.05 REMARK 500 HIS B 232 -162.89 -169.46 REMARK 500 LYS B 288 157.47 156.59 REMARK 500 PRO B 309 -176.53 -65.71 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 D8C A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAD A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue D8C B 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAD B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 B 502 DBREF 6KG2 A 36 338 UNP P13995 MTDC_HUMAN 36 338 DBREF 6KG2 B 36 338 UNP P13995 MTDC_HUMAN 36 338 SEQADV 6KG2 MET A 16 UNP P13995 EXPRESSION TAG SEQADV 6KG2 GLY A 17 UNP P13995 EXPRESSION TAG SEQADV 6KG2 SER A 18 UNP P13995 EXPRESSION TAG SEQADV 6KG2 SER A 19 UNP P13995 EXPRESSION TAG SEQADV 6KG2 HIS A 20 UNP P13995 EXPRESSION TAG SEQADV 6KG2 HIS A 21 UNP P13995 EXPRESSION TAG SEQADV 6KG2 HIS A 22 UNP P13995 EXPRESSION TAG SEQADV 6KG2 HIS A 23 UNP P13995 EXPRESSION TAG SEQADV 6KG2 HIS A 24 UNP P13995 EXPRESSION TAG SEQADV 6KG2 HIS A 25 UNP P13995 EXPRESSION TAG SEQADV 6KG2 SER A 26 UNP P13995 EXPRESSION TAG SEQADV 6KG2 SER A 27 UNP P13995 EXPRESSION TAG SEQADV 6KG2 GLY A 28 UNP P13995 EXPRESSION TAG SEQADV 6KG2 GLU A 29 UNP P13995 EXPRESSION TAG SEQADV 6KG2 ASN A 30 UNP P13995 EXPRESSION TAG SEQADV 6KG2 LEU A 31 UNP P13995 EXPRESSION TAG SEQADV 6KG2 TYR A 32 UNP P13995 EXPRESSION TAG SEQADV 6KG2 PHE A 33 UNP P13995 EXPRESSION TAG SEQADV 6KG2 GLN A 34 UNP P13995 EXPRESSION TAG SEQADV 6KG2 GLY A 35 UNP P13995 EXPRESSION TAG SEQADV 6KG2 MET B 16 UNP P13995 EXPRESSION TAG SEQADV 6KG2 GLY B 17 UNP P13995 EXPRESSION TAG SEQADV 6KG2 SER B 18 UNP P13995 EXPRESSION TAG SEQADV 6KG2 SER B 19 UNP P13995 EXPRESSION TAG SEQADV 6KG2 HIS B 20 UNP P13995 EXPRESSION TAG SEQADV 6KG2 HIS B 21 UNP P13995 EXPRESSION TAG SEQADV 6KG2 HIS B 22 UNP P13995 EXPRESSION TAG SEQADV 6KG2 HIS B 23 UNP P13995 EXPRESSION TAG SEQADV 6KG2 HIS B 24 UNP P13995 EXPRESSION TAG SEQADV 6KG2 HIS B 25 UNP P13995 EXPRESSION TAG SEQADV 6KG2 SER B 26 UNP P13995 EXPRESSION TAG SEQADV 6KG2 SER B 27 UNP P13995 EXPRESSION TAG SEQADV 6KG2 GLY B 28 UNP P13995 EXPRESSION TAG SEQADV 6KG2 GLU B 29 UNP P13995 EXPRESSION TAG SEQADV 6KG2 ASN B 30 UNP P13995 EXPRESSION TAG SEQADV 6KG2 LEU B 31 UNP P13995 EXPRESSION TAG SEQADV 6KG2 TYR B 32 UNP P13995 EXPRESSION TAG SEQADV 6KG2 PHE B 33 UNP P13995 EXPRESSION TAG SEQADV 6KG2 GLN B 34 UNP P13995 EXPRESSION TAG SEQADV 6KG2 GLY B 35 UNP P13995 EXPRESSION TAG SEQRES 1 A 323 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 323 GLU ASN LEU TYR PHE GLN GLY GLU ALA VAL VAL ILE SER SEQRES 3 A 323 GLY ARG LYS LEU ALA GLN GLN ILE LYS GLN GLU VAL ARG SEQRES 4 A 323 GLN GLU VAL GLU GLU TRP VAL ALA SER GLY ASN LYS ARG SEQRES 5 A 323 PRO HIS LEU SER VAL ILE LEU VAL GLY GLU ASN PRO ALA SEQRES 6 A 323 SER HIS SER TYR VAL LEU ASN LYS THR ARG ALA ALA ALA SEQRES 7 A 323 VAL VAL GLY ILE ASN SER GLU THR ILE MET LYS PRO ALA SEQRES 8 A 323 SER ILE SER GLU GLU GLU LEU LEU ASN LEU ILE ASN LYS SEQRES 9 A 323 LEU ASN ASN ASP ASP ASN VAL ASP GLY LEU LEU VAL GLN SEQRES 10 A 323 LEU PRO LEU PRO GLU HIS ILE ASP GLU ARG ARG ILE CYS SEQRES 11 A 323 ASN ALA VAL SER PRO ASP LYS ASP VAL ASP GLY PHE HIS SEQRES 12 A 323 VAL ILE ASN VAL GLY ARG MET CYS LEU ASP GLN TYR SER SEQRES 13 A 323 MET LEU PRO ALA THR PRO TRP GLY VAL TRP GLU ILE ILE SEQRES 14 A 323 LYS ARG THR GLY ILE PRO THR LEU GLY LYS ASN VAL VAL SEQRES 15 A 323 VAL ALA GLY ARG SER LYS ASN VAL GLY MET PRO ILE ALA SEQRES 16 A 323 MET LEU LEU HIS THR ASP GLY ALA HIS GLU ARG PRO GLY SEQRES 17 A 323 GLY ASP ALA THR VAL THR ILE SER HIS ARG TYR THR PRO SEQRES 18 A 323 LYS GLU GLN LEU LYS LYS HIS THR ILE LEU ALA ASP ILE SEQRES 19 A 323 VAL ILE SER ALA ALA GLY ILE PRO ASN LEU ILE THR ALA SEQRES 20 A 323 ASP MET ILE LYS GLU GLY ALA ALA VAL ILE ASP VAL GLY SEQRES 21 A 323 ILE ASN ARG VAL HIS ASP PRO VAL THR ALA LYS PRO LYS SEQRES 22 A 323 LEU VAL GLY ASP VAL ASP PHE GLU GLY VAL ARG GLN LYS SEQRES 23 A 323 ALA GLY TYR ILE THR PRO VAL PRO GLY GLY VAL GLY PRO SEQRES 24 A 323 MET THR VAL ALA MET LEU MET LYS ASN THR ILE ILE ALA SEQRES 25 A 323 ALA LYS LYS VAL LEU ARG LEU GLU GLU ARG GLU SEQRES 1 B 323 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 323 GLU ASN LEU TYR PHE GLN GLY GLU ALA VAL VAL ILE SER SEQRES 3 B 323 GLY ARG LYS LEU ALA GLN GLN ILE LYS GLN GLU VAL ARG SEQRES 4 B 323 GLN GLU VAL GLU GLU TRP VAL ALA SER GLY ASN LYS ARG SEQRES 5 B 323 PRO HIS LEU SER VAL ILE LEU VAL GLY GLU ASN PRO ALA SEQRES 6 B 323 SER HIS SER TYR VAL LEU ASN LYS THR ARG ALA ALA ALA SEQRES 7 B 323 VAL VAL GLY ILE ASN SER GLU THR ILE MET LYS PRO ALA SEQRES 8 B 323 SER ILE SER GLU GLU GLU LEU LEU ASN LEU ILE ASN LYS SEQRES 9 B 323 LEU ASN ASN ASP ASP ASN VAL ASP GLY LEU LEU VAL GLN SEQRES 10 B 323 LEU PRO LEU PRO GLU HIS ILE ASP GLU ARG ARG ILE CYS SEQRES 11 B 323 ASN ALA VAL SER PRO ASP LYS ASP VAL ASP GLY PHE HIS SEQRES 12 B 323 VAL ILE ASN VAL GLY ARG MET CYS LEU ASP GLN TYR SER SEQRES 13 B 323 MET LEU PRO ALA THR PRO TRP GLY VAL TRP GLU ILE ILE SEQRES 14 B 323 LYS ARG THR GLY ILE PRO THR LEU GLY LYS ASN VAL VAL SEQRES 15 B 323 VAL ALA GLY ARG SER LYS ASN VAL GLY MET PRO ILE ALA SEQRES 16 B 323 MET LEU LEU HIS THR ASP GLY ALA HIS GLU ARG PRO GLY SEQRES 17 B 323 GLY ASP ALA THR VAL THR ILE SER HIS ARG TYR THR PRO SEQRES 18 B 323 LYS GLU GLN LEU LYS LYS HIS THR ILE LEU ALA ASP ILE SEQRES 19 B 323 VAL ILE SER ALA ALA GLY ILE PRO ASN LEU ILE THR ALA SEQRES 20 B 323 ASP MET ILE LYS GLU GLY ALA ALA VAL ILE ASP VAL GLY SEQRES 21 B 323 ILE ASN ARG VAL HIS ASP PRO VAL THR ALA LYS PRO LYS SEQRES 22 B 323 LEU VAL GLY ASP VAL ASP PHE GLU GLY VAL ARG GLN LYS SEQRES 23 B 323 ALA GLY TYR ILE THR PRO VAL PRO GLY GLY VAL GLY PRO SEQRES 24 B 323 MET THR VAL ALA MET LEU MET LYS ASN THR ILE ILE ALA SEQRES 25 B 323 ALA LYS LYS VAL LEU ARG LEU GLU GLU ARG GLU HET D8C A 500 37 HET NAD A 501 44 HET PO4 A 502 5 HET D8C B 500 37 HET NAD B 501 44 HET PO4 B 502 5 HETNAM D8C N-[2-CHLORANYL-4-[[7-METHYL-8-(4-METHYLPIPERAZIN-1-YL)- HETNAM 2 D8C 5-OXIDANYLIDENE-2,4-DIHYDRO-1H-CHROMENO[3,4-C]PYRIDIN- HETNAM 3 D8C 3-YL]CARBONYL]PHENYL]METHANESULFONAMIDE HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM PO4 PHOSPHATE ION FORMUL 3 D8C 2(C26 H29 CL N4 O5 S) FORMUL 4 NAD 2(C21 H27 N7 O14 P2) FORMUL 5 PO4 2(O4 P 3-) FORMUL 9 HOH *103(H2 O) HELIX 1 AA1 SER A 41 SER A 63 1 23 HELIX 2 AA2 ASN A 78 VAL A 95 1 18 HELIX 3 AA3 SER A 109 ASP A 123 1 15 HELIX 4 AA4 ASP A 140 ASN A 146 1 7 HELIX 5 AA5 SER A 149 ASP A 153 5 5 HELIX 6 AA6 HIS A 158 LEU A 167 1 10 HELIX 7 AA7 PRO A 174 THR A 187 1 14 HELIX 8 AA8 VAL A 205 THR A 215 1 11 HELIX 9 AA9 PRO A 236 ILE A 245 1 10 HELIX 10 AB1 ASP A 294 ALA A 302 1 9 HELIX 11 AB2 GLY A 311 LYS A 329 1 19 HELIX 12 AB3 SER B 41 SER B 63 1 23 HELIX 13 AB4 ASN B 78 VAL B 95 1 18 HELIX 14 AB5 SER B 109 ASP B 123 1 15 HELIX 15 AB6 ASP B 140 ASN B 146 1 7 HELIX 16 AB7 SER B 149 ASP B 153 5 5 HELIX 17 AB8 HIS B 158 LEU B 167 1 10 HELIX 18 AB9 PRO B 174 GLY B 188 1 15 HELIX 19 AC1 VAL B 205 THR B 215 1 11 HELIX 20 AC2 PRO B 236 ILE B 245 1 10 HELIX 21 AC3 ASP B 294 GLN B 300 1 7 HELIX 22 AC4 GLY B 311 LYS B 330 1 20 SHEET 1 AA112 VAL A 38 VAL A 39 0 SHEET 2 AA112 TYR A 304 ILE A 305 1 O ILE A 305 N VAL A 38 SHEET 3 AA112 ALA A 270 ASP A 273 1 N VAL A 271 O TYR A 304 SHEET 4 AA112 ILE A 249 SER A 252 1 N VAL A 250 O ILE A 272 SHEET 5 AA112 ASN A 195 ALA A 199 1 N VAL A 197 O ILE A 251 SHEET 6 AA112 THR A 227 SER A 231 1 O THR A 229 N VAL A 196 SHEET 7 AA112 THR B 227 SER B 231 -1 O VAL B 228 N ILE A 230 SHEET 8 AA112 ASN B 195 ALA B 199 1 N VAL B 196 O THR B 227 SHEET 9 AA112 ILE B 249 SER B 252 1 O ILE B 251 N VAL B 197 SHEET 10 AA112 ALA B 270 ASP B 273 1 O ILE B 272 N SER B 252 SHEET 11 AA112 TYR B 304 ILE B 305 1 O TYR B 304 N VAL B 271 SHEET 12 AA112 VAL B 38 VAL B 39 1 N VAL B 38 O ILE B 305 SHEET 1 AA2 3 ASN A 98 LYS A 104 0 SHEET 2 AA2 3 HIS A 69 VAL A 75 1 N VAL A 72 O ILE A 102 SHEET 3 AA2 3 GLY A 128 VAL A 131 1 O LEU A 130 N SER A 71 SHEET 1 AA3 3 ASN B 98 LYS B 104 0 SHEET 2 AA3 3 HIS B 69 VAL B 75 1 N LEU B 70 O ASN B 98 SHEET 3 AA3 3 GLY B 128 VAL B 131 1 O GLY B 128 N SER B 71 SHEET 1 AA4 2 ASN B 277 ARG B 278 0 SHEET 2 AA4 2 LEU B 289 VAL B 290 -1 O VAL B 290 N ASN B 277 CISPEP 1 LEU A 133 PRO A 134 0 6.84 CISPEP 2 VAL A 308 PRO A 309 0 -7.58 CISPEP 3 LEU B 133 PRO B 134 0 8.13 CISPEP 4 VAL B 308 PRO B 309 0 0.59 SITE 1 AC1 13 ARG A 43 TYR A 84 ASN A 87 LYS A 88 SITE 2 AC1 13 GLN A 132 LEU A 133 PRO A 309 GLY A 310 SITE 3 AC1 13 GLY A 313 PRO A 314 VAL A 317 NAD A 501 SITE 4 AC1 13 HOH A 609 SITE 1 AC2 23 THR A 176 GLY A 200 ARG A 201 SER A 202 SITE 2 AC2 23 ASN A 204 VAL A 205 HIS A 232 ARG A 233 SITE 3 AC2 23 ALA A 253 ALA A 254 GLY A 255 ILE A 256 SITE 4 AC2 23 LEU A 259 VAL A 274 GLY A 275 ILE A 276 SITE 5 AC2 23 VAL A 312 GLY A 313 THR A 316 D8C A 500 SITE 6 AC2 23 PO4 A 502 HOH A 610 HOH A 639 SITE 1 AC3 7 ARG A 201 ARG A 233 NAD A 501 HOH A 607 SITE 2 AC3 7 HOH A 627 ASP B 216 HIS B 219 SITE 1 AC4 13 TYR B 84 ASN B 87 LYS B 88 GLN B 132 SITE 2 AC4 13 LEU B 133 ILE B 276 PRO B 309 GLY B 310 SITE 3 AC4 13 GLY B 313 PRO B 314 VAL B 317 NAD B 501 SITE 4 AC4 13 HOH B 631 SITE 1 AC5 23 THR B 176 GLY B 200 ARG B 201 SER B 202 SITE 2 AC5 23 ASN B 204 VAL B 205 HIS B 232 ARG B 233 SITE 3 AC5 23 ALA B 253 ALA B 254 GLY B 255 ILE B 256 SITE 4 AC5 23 LEU B 259 VAL B 274 GLY B 275 ILE B 276 SITE 5 AC5 23 VAL B 312 GLY B 313 THR B 316 D8C B 500 SITE 6 AC5 23 PO4 B 502 HOH B 632 HOH B 642 SITE 1 AC6 6 ASP A 216 HIS A 219 ARG B 201 ARG B 233 SITE 2 AC6 6 NAD B 501 HOH B 632 CRYST1 116.992 116.992 112.869 90.00 90.00 120.00 P 65 12 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 0.008548 0.004935 0.000000 0.00000 SCALE2 0.000000 0.009870 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008860 0.00000