HEADER TRANSFERASE 22-MAR-21 7NY9 TITLE CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC BRANCHED-CHAIN AMINOTRANSFERASE TITLE 2 (BCAT1) IN COMPLEX WITH PLP AND SMALL MOLECULE INHIBITOR COMPOUND 38 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BRANCHED-CHAIN-AMINO-ACID AMINOTRANSFERASE, CYTOSOLIC; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: BCAT(C),PROTEIN ECA39, BCAT1; COMPND 5 EC: 2.6.1.42; 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: BCAT1, BCT1, ECA39; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS BRANCHED-CHAIN-AMINO-ACID AMINOTRANSFERASE, PYRIDOXAL-PHOSPHATE- KEYWDS 2 DEPENDENT AMINOTRANSFERASE, TRANSFERASE, SMALL MOLECULE INHIBITOR EXPDTA X-RAY DIFFRACTION AUTHOR R.C.HILLIG REVDAT 3 31-JAN-24 7NY9 1 REMARK REVDAT 2 23-NOV-22 7NY9 1 JRNL REVDAT 1 02-NOV-22 7NY9 0 JRNL AUTH J.GUNTHER,R.C.HILLIG,K.ZIMMERMANN,S.KAULFUSS,C.LEMOS, JRNL AUTH 2 D.NGUYEN,H.REHWINKEL,M.HABGOOD,C.LECHNER,R.NEUHAUS,U.GANZER, JRNL AUTH 3 M.DREWES,J.CHAI,L.BOUCHE JRNL TITL BAY-069, A NOVEL (TRIFLUOROMETHYL)PYRIMIDINEDIONE-BASED JRNL TITL 2 BCAT1/2 INHIBITOR AND CHEMICAL PROBE. JRNL REF J.MED.CHEM. V. 65 14366 2022 JRNL REFN ISSN 0022-2623 JRNL PMID 36261130 JRNL DOI 10.1021/ACS.JMEDCHEM.2C00441 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.32 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 97447 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) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2101 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 7074 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.22 REMARK 3 BIN R VALUE (WORKING SET) : 0.2850 REMARK 3 BIN FREE R VALUE SET COUNT : 153 REMARK 3 BIN FREE R VALUE : 0.2920 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5772 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 94 REMARK 3 SOLVENT ATOMS : 865 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.38000 REMARK 3 B22 (A**2) : 1.57000 REMARK 3 B33 (A**2) : 1.81000 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): 0.087 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.087 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.072 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.175 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.952 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6106 ; 0.005 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 5700 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8335 ; 1.257 ; 1.661 REMARK 3 BOND ANGLES OTHERS (DEGREES): 13148 ; 1.251 ; 1.578 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 752 ; 6.657 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 297 ;34.895 ;22.593 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1018 ;12.204 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 33 ;16.537 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 774 ; 0.058 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6863 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1365 ; 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 23 385 B 23 385 11626 0.090 0.050 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 23 A 386 REMARK 3 ORIGIN FOR THE GROUP (A): -36.4160 -6.7410 -17.6950 REMARK 3 T TENSOR REMARK 3 T11: 0.1720 T22: 0.0601 REMARK 3 T33: 0.0399 T12: -0.0270 REMARK 3 T13: 0.0104 T23: -0.0336 REMARK 3 L TENSOR REMARK 3 L11: 0.5868 L22: 0.3013 REMARK 3 L33: 0.4692 L12: 0.0843 REMARK 3 L13: 0.1460 L23: 0.0254 REMARK 3 S TENSOR REMARK 3 S11: 0.0055 S12: 0.0312 S13: -0.1080 REMARK 3 S21: 0.0019 S22: -0.0344 S23: 0.0072 REMARK 3 S31: 0.0872 S32: -0.1401 S33: 0.0289 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 : B 21 B 386 REMARK 3 ORIGIN FOR THE GROUP (A): -11.2500 11.5140 -4.6580 REMARK 3 T TENSOR REMARK 3 T11: 0.1655 T22: 0.0053 REMARK 3 T33: 0.0059 T12: -0.0034 REMARK 3 T13: -0.0139 T23: 0.0043 REMARK 3 L TENSOR REMARK 3 L11: 0.5306 L22: 0.2553 REMARK 3 L33: 0.5779 L12: 0.1362 REMARK 3 L13: -0.2165 L23: -0.1795 REMARK 3 S TENSOR REMARK 3 S11: -0.0037 S12: -0.0273 S13: -0.0210 REMARK 3 S21: 0.0293 S22: -0.0278 S23: -0.0366 REMARK 3 S31: -0.0424 S32: 0.0517 S33: 0.0315 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 7NY9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-MAR-21. REMARK 100 THE DEPOSITION ID IS D_1292114796. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-JUL-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, DESY REMARK 200 BEAMLINE : P11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0332 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS VERSION NOV 1, 2016 REMARK 200 DATA SCALING SOFTWARE : POINTLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 99549 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 48.320 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 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 FOR SHELL : 1.700 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: 2ABJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN AT 17 MG/ML IN 10 MILLIMOLAR REMARK 280 TRIS-HCL PH 8.0, 100 MILLIMOLAR NACL, 3 MILLIMOLAR DTT. PROTEIN REMARK 280 PREINCUBATED OVER NIGHT AT 293 K WITH 10 MILLIMOLAR 3-PHENYL- REMARK 280 PROPIONATE, 3 MILLIMOLAR DTT AND 1.5 MILLIMOLAR PLP. DROPS MADE REMARK 280 FROM 1 MICROLITER PROTEIN AND 1 MICROLITER RESERVOIR (225 REMARK 280 MILLIMOLAR MGCL2, 16-20 % (W/V) PEG 3350). INHIBITOR SOAKED INTO REMARK 280 PREFORMED CRYSTALS FOR 3 DAYS AT 10 MILLIMOLAR. CRYO: RESERVOIR REMARK 280 SOLUTION COMPLEMENTED WITH 20 % (V/V) GLYCEROL AND 10 MILLIMOLAR REMARK 280 INHIBITOR., VAPOR DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 33.21250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.71600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 51.50050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.71600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.21250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 51.50050 REMARK 290 SMTRY3 4 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6050 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26530 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -39.0 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 GLY A -2 REMARK 465 PRO A -1 REMARK 465 GLY A 0 REMARK 465 MET A 1 REMARK 465 LYS A 2 REMARK 465 ASP A 3 REMARK 465 CYS A 4 REMARK 465 SER A 5 REMARK 465 ASN A 6 REMARK 465 GLY A 7 REMARK 465 CYS A 8 REMARK 465 SER A 9 REMARK 465 ALA A 10 REMARK 465 GLU A 11 REMARK 465 CYS A 12 REMARK 465 THR A 13 REMARK 465 GLY A 14 REMARK 465 GLU A 15 REMARK 465 GLY A 16 REMARK 465 GLY A 17 REMARK 465 SER A 18 REMARK 465 LYS A 19 REMARK 465 GLU A 20 REMARK 465 VAL A 21 REMARK 465 VAL A 22 REMARK 465 GLY B -2 REMARK 465 PRO B -1 REMARK 465 GLY B 0 REMARK 465 MET B 1 REMARK 465 LYS B 2 REMARK 465 ASP B 3 REMARK 465 CYS B 4 REMARK 465 SER B 5 REMARK 465 ASN B 6 REMARK 465 GLY B 7 REMARK 465 CYS B 8 REMARK 465 SER B 9 REMARK 465 ALA B 10 REMARK 465 GLU B 11 REMARK 465 CYS B 12 REMARK 465 THR B 13 REMARK 465 GLY B 14 REMARK 465 GLU B 15 REMARK 465 GLY B 16 REMARK 465 GLY B 17 REMARK 465 SER B 18 REMARK 465 LYS B 19 REMARK 465 GLU B 20 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 OH TYR A 193 O HOH A 501 2.05 REMARK 500 OE1 GLU A 69 O HOH A 502 2.14 REMARK 500 O HOH B 570 O HOH B 803 2.14 REMARK 500 O23 UV5 A 401 O HOH A 501 2.15 REMARK 500 O23 UV5 B 401 O HOH B 502 2.16 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 LYS A 222 58.02 -90.19 REMARK 500 VAL A 336 -77.50 68.13 REMARK 500 VAL B 336 -77.23 68.62 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 929 DISTANCE = 6.02 ANGSTROMS REMARK 525 HOH A 930 DISTANCE = 6.43 ANGSTROMS REMARK 525 HOH A 931 DISTANCE = 7.16 ANGSTROMS 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 MG A 403 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 572 O REMARK 620 2 HOH A 594 O 92.7 REMARK 620 3 HOH A 597 O 83.8 176.0 REMARK 620 4 HOH A 601 O 89.9 87.6 90.5 REMARK 620 5 HOH A 798 O 173.0 94.3 89.2 90.2 REMARK 620 6 HOH A 885 O 95.5 88.3 93.9 173.4 84.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 403 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 133 OD2 REMARK 620 2 HOH B 511 O 97.9 REMARK 620 3 HOH B 519 O 80.2 91.3 REMARK 620 4 HOH B 535 O 97.9 86.9 177.2 REMARK 620 5 HOH B 578 O 173.4 84.2 93.6 88.4 REMARK 620 6 HOH B 602 O 88.1 172.6 94.0 88.1 90.3 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7NTR RELATED DB: PDB REMARK 900 RELATED ID: 7NWA RELATED DB: PDB REMARK 900 RELATED ID: 7NWB RELATED DB: PDB REMARK 900 RELATED ID: 7NWC RELATED DB: PDB REMARK 900 RELATED ID: 7NWE RELATED DB: PDB REMARK 900 RELATED ID: 7NWM RELATED DB: PDB REMARK 900 RELATED ID: 7NXN RELATED DB: PDB REMARK 900 RELATED ID: 7NXO RELATED DB: PDB REMARK 900 RELATED ID: 7NY2 RELATED DB: PDB DBREF 7NY9 A 1 386 UNP P54687 BCAT1_HUMAN 1 386 DBREF 7NY9 B 1 386 UNP P54687 BCAT1_HUMAN 1 386 SEQADV 7NY9 GLY A -2 UNP P54687 EXPRESSION TAG SEQADV 7NY9 PRO A -1 UNP P54687 EXPRESSION TAG SEQADV 7NY9 GLY A 0 UNP P54687 EXPRESSION TAG SEQADV 7NY9 ARG A 379 UNP P54687 SER 379 ENGINEERED MUTATION SEQADV 7NY9 GLY B -2 UNP P54687 EXPRESSION TAG SEQADV 7NY9 PRO B -1 UNP P54687 EXPRESSION TAG SEQADV 7NY9 GLY B 0 UNP P54687 EXPRESSION TAG SEQADV 7NY9 ARG B 379 UNP P54687 SER 379 ENGINEERED MUTATION SEQRES 1 A 389 GLY PRO GLY MET LYS ASP CYS SER ASN GLY CYS SER ALA SEQRES 2 A 389 GLU CYS THR GLY GLU GLY GLY SER LYS GLU VAL VAL GLY SEQRES 3 A 389 THR PHE LYS ALA LYS ASP LEU ILE VAL THR PRO ALA THR SEQRES 4 A 389 ILE LEU LYS GLU LYS PRO ASP PRO ASN ASN LEU VAL PHE SEQRES 5 A 389 GLY THR VAL PHE THR ASP HIS MET LEU THR VAL GLU TRP SEQRES 6 A 389 SER SER GLU PHE GLY TRP GLU LYS PRO HIS ILE LYS PRO SEQRES 7 A 389 LEU GLN ASN LEU SER LEU HIS PRO GLY SER SER ALA LEU SEQRES 8 A 389 HIS TYR ALA VAL GLU LEU PHE GLU GLY LEU LYS ALA PHE SEQRES 9 A 389 ARG GLY VAL ASP ASN LYS ILE ARG LEU PHE GLN PRO ASN SEQRES 10 A 389 LEU ASN MET ASP ARG MET TYR ARG SER ALA VAL ARG ALA SEQRES 11 A 389 THR LEU PRO VAL PHE ASP LYS GLU GLU LEU LEU GLU CYS SEQRES 12 A 389 ILE GLN GLN LEU VAL LYS LEU ASP GLN GLU TRP VAL PRO SEQRES 13 A 389 TYR SER THR SER ALA SER LEU TYR ILE ARG PRO THR PHE SEQRES 14 A 389 ILE GLY THR GLU PRO SER LEU GLY VAL LYS LYS PRO THR SEQRES 15 A 389 LYS ALA LEU LEU PHE VAL LEU LEU SER PRO VAL GLY PRO SEQRES 16 A 389 TYR PHE SER SER GLY THR PHE ASN PRO VAL SER LEU TRP SEQRES 17 A 389 ALA ASN PRO LYS TYR VAL ARG ALA TRP LYS GLY GLY THR SEQRES 18 A 389 GLY ASP CYS LYS MET GLY GLY ASN TYR GLY SER SER LEU SEQRES 19 A 389 PHE ALA GLN CYS GLU ALA VAL ASP ASN GLY CYS GLN GLN SEQRES 20 A 389 VAL LEU TRP LEU TYR GLY GLU ASP HIS GLN ILE THR GLU SEQRES 21 A 389 VAL GLY THR MET ASN LEU PHE LEU TYR TRP ILE ASN GLU SEQRES 22 A 389 ASP GLY GLU GLU GLU LEU ALA THR PRO PRO LEU ASP GLY SEQRES 23 A 389 ILE ILE LEU PRO GLY VAL THR ARG ARG CYS ILE LEU ASP SEQRES 24 A 389 LEU ALA HIS GLN TRP GLY GLU PHE LYS VAL SER GLU ARG SEQRES 25 A 389 TYR LEU THR MET ASP ASP LEU THR THR ALA LEU GLU GLY SEQRES 26 A 389 ASN ARG VAL ARG GLU MET PHE GLY SER GLY THR ALA CYS SEQRES 27 A 389 VAL VAL CYS PRO VAL SER ASP ILE LEU TYR LYS GLY GLU SEQRES 28 A 389 THR ILE HIS ILE PRO THR MET GLU ASN GLY PRO LYS LEU SEQRES 29 A 389 ALA SER ARG ILE LEU SER LYS LEU THR ASP ILE GLN TYR SEQRES 30 A 389 GLY ARG GLU GLU ARG ASP TRP THR ILE VAL LEU SER SEQRES 1 B 389 GLY PRO GLY MET LYS ASP CYS SER ASN GLY CYS SER ALA SEQRES 2 B 389 GLU CYS THR GLY GLU GLY GLY SER LYS GLU VAL VAL GLY SEQRES 3 B 389 THR PHE LYS ALA LYS ASP LEU ILE VAL THR PRO ALA THR SEQRES 4 B 389 ILE LEU LYS GLU LYS PRO ASP PRO ASN ASN LEU VAL PHE SEQRES 5 B 389 GLY THR VAL PHE THR ASP HIS MET LEU THR VAL GLU TRP SEQRES 6 B 389 SER SER GLU PHE GLY TRP GLU LYS PRO HIS ILE LYS PRO SEQRES 7 B 389 LEU GLN ASN LEU SER LEU HIS PRO GLY SER SER ALA LEU SEQRES 8 B 389 HIS TYR ALA VAL GLU LEU PHE GLU GLY LEU LYS ALA PHE SEQRES 9 B 389 ARG GLY VAL ASP ASN LYS ILE ARG LEU PHE GLN PRO ASN SEQRES 10 B 389 LEU ASN MET ASP ARG MET TYR ARG SER ALA VAL ARG ALA SEQRES 11 B 389 THR LEU PRO VAL PHE ASP LYS GLU GLU LEU LEU GLU CYS SEQRES 12 B 389 ILE GLN GLN LEU VAL LYS LEU ASP GLN GLU TRP VAL PRO SEQRES 13 B 389 TYR SER THR SER ALA SER LEU TYR ILE ARG PRO THR PHE SEQRES 14 B 389 ILE GLY THR GLU PRO SER LEU GLY VAL LYS LYS PRO THR SEQRES 15 B 389 LYS ALA LEU LEU PHE VAL LEU LEU SER PRO VAL GLY PRO SEQRES 16 B 389 TYR PHE SER SER GLY THR PHE ASN PRO VAL SER LEU TRP SEQRES 17 B 389 ALA ASN PRO LYS TYR VAL ARG ALA TRP LYS GLY GLY THR SEQRES 18 B 389 GLY ASP CYS LYS MET GLY GLY ASN TYR GLY SER SER LEU SEQRES 19 B 389 PHE ALA GLN CYS GLU ALA VAL ASP ASN GLY CYS GLN GLN SEQRES 20 B 389 VAL LEU TRP LEU TYR GLY GLU ASP HIS GLN ILE THR GLU SEQRES 21 B 389 VAL GLY THR MET ASN LEU PHE LEU TYR TRP ILE ASN GLU SEQRES 22 B 389 ASP GLY GLU GLU GLU LEU ALA THR PRO PRO LEU ASP GLY SEQRES 23 B 389 ILE ILE LEU PRO GLY VAL THR ARG ARG CYS ILE LEU ASP SEQRES 24 B 389 LEU ALA HIS GLN TRP GLY GLU PHE LYS VAL SER GLU ARG SEQRES 25 B 389 TYR LEU THR MET ASP ASP LEU THR THR ALA LEU GLU GLY SEQRES 26 B 389 ASN ARG VAL ARG GLU MET PHE GLY SER GLY THR ALA CYS SEQRES 27 B 389 VAL VAL CYS PRO VAL SER ASP ILE LEU TYR LYS GLY GLU SEQRES 28 B 389 THR ILE HIS ILE PRO THR MET GLU ASN GLY PRO LYS LEU SEQRES 29 B 389 ALA SER ARG ILE LEU SER LYS LEU THR ASP ILE GLN TYR SEQRES 30 B 389 GLY ARG GLU GLU ARG ASP TRP THR ILE VAL LEU SER HET UV5 A 401 31 HET PLP A 402 15 HET MG A 403 1 HET UV5 B 401 31 HET PLP B 402 15 HET MG B 403 1 HETNAM UV5 3-[2,6-BIS(OXIDANYLIDENE)-4-(TRIFLUOROMETHYL)-5~{H}- HETNAM 2 UV5 PYRIMIDIN-1-YL]-~{N}-METHYL-2-PYRIDIN-2-YL-IMIDAZO[1, HETNAM 3 UV5 2-A]PYRIDINE-7-CARBOXAMIDE HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETNAM MG MAGNESIUM ION HETSYN PLP VITAMIN B6 PHOSPHATE FORMUL 3 UV5 2(C19 H13 F3 N6 O3) FORMUL 4 PLP 2(C8 H10 N O6 P) FORMUL 5 MG 2(MG 2+) FORMUL 9 HOH *865(H2 O) HELIX 1 AA1 LYS A 26 LEU A 30 5 5 HELIX 2 AA2 SER A 85 TYR A 90 1 6 HELIX 3 AA3 GLN A 112 THR A 128 1 17 HELIX 4 AA4 ASP A 133 ASP A 148 1 16 HELIX 5 AA5 GLN A 149 VAL A 152 5 4 HELIX 6 AA6 GLY A 224 SER A 229 1 6 HELIX 7 AA7 SER A 230 ASN A 240 1 11 HELIX 8 AA8 GLY A 288 GLY A 302 1 15 HELIX 9 AA9 THR A 312 GLY A 322 1 11 HELIX 10 AB1 PRO A 353 GLY A 358 5 6 HELIX 11 AB2 PRO A 359 TYR A 374 1 16 HELIX 12 AB3 LYS B 26 LEU B 30 5 5 HELIX 13 AB4 SER B 85 TYR B 90 1 6 HELIX 14 AB5 GLN B 112 THR B 128 1 17 HELIX 15 AB6 ASP B 133 ASP B 148 1 16 HELIX 16 AB7 GLN B 149 VAL B 152 5 4 HELIX 17 AB8 GLY B 224 SER B 229 1 6 HELIX 18 AB9 SER B 230 ASN B 240 1 11 HELIX 19 AC1 GLY B 288 GLY B 302 1 15 HELIX 20 AC2 THR B 312 GLY B 322 1 11 HELIX 21 AC3 PRO B 353 GLY B 358 5 6 HELIX 22 AC4 PRO B 359 TYR B 374 1 16 SHEET 1 AA1 6 ILE A 31 VAL A 32 0 SHEET 2 AA1 6 HIS A 72 PRO A 75 1 O ILE A 73 N ILE A 31 SHEET 3 AA1 6 HIS A 56 SER A 63 -1 N THR A 59 O HIS A 72 SHEET 4 AA1 6 LYS A 180 VAL A 190 -1 O LEU A 183 N VAL A 60 SHEET 5 AA1 6 SER A 159 GLY A 168 -1 N TYR A 161 O SER A 188 SHEET 6 AA1 6 GLU A 93 PHE A 95 -1 N LEU A 94 O PHE A 166 SHEET 1 AA2 7 GLY A 67 TRP A 68 0 SHEET 2 AA2 7 HIS A 56 SER A 63 -1 N SER A 63 O GLY A 67 SHEET 3 AA2 7 LYS A 180 VAL A 190 -1 O LEU A 183 N VAL A 60 SHEET 4 AA2 7 SER A 159 GLY A 168 -1 N TYR A 161 O SER A 188 SHEET 5 AA2 7 LEU A 98 ARG A 102 -1 N LEU A 98 O ILE A 162 SHEET 6 AA2 7 ILE A 108 PHE A 111 -1 O ARG A 109 N PHE A 101 SHEET 7 AA2 7 THR A 382 VAL A 384 -1 O ILE A 383 N LEU A 110 SHEET 1 AA3 2 LEU A 79 LEU A 81 0 SHEET 2 AA3 2 LEU B 79 LEU B 81 -1 O LEU B 79 N LEU A 81 SHEET 1 AA4 8 LYS A 305 GLU A 308 0 SHEET 2 AA4 8 GLU A 274 THR A 278 1 N LEU A 276 O LYS A 305 SHEET 3 AA4 8 MET A 261 ILE A 268 -1 N LEU A 265 O ALA A 277 SHEET 4 AA4 8 GLN A 254 VAL A 258 -1 N VAL A 258 O MET A 261 SHEET 5 AA4 8 GLN A 244 TYR A 249 -1 N TYR A 249 O GLN A 254 SHEET 6 AA4 8 VAL A 202 TRP A 205 1 N TRP A 205 O LEU A 246 SHEET 7 AA4 8 VAL A 336 TYR A 345 1 O LEU A 344 N LEU A 204 SHEET 8 AA4 8 GLU A 348 HIS A 351 -1 O ILE A 350 N ILE A 343 SHEET 1 AA5 6 LYS A 305 GLU A 308 0 SHEET 2 AA5 6 GLU A 274 THR A 278 1 N LEU A 276 O LYS A 305 SHEET 3 AA5 6 MET A 261 ILE A 268 -1 N LEU A 265 O ALA A 277 SHEET 4 AA5 6 VAL A 325 GLY A 332 -1 O GLU A 327 N TYR A 266 SHEET 5 AA5 6 VAL A 336 TYR A 345 -1 O VAL A 336 N GLY A 332 SHEET 6 AA5 6 GLU A 348 HIS A 351 -1 O ILE A 350 N ILE A 343 SHEET 1 AA6 6 ILE B 31 VAL B 32 0 SHEET 2 AA6 6 HIS B 72 PRO B 75 1 O ILE B 73 N ILE B 31 SHEET 3 AA6 6 HIS B 56 SER B 63 -1 N THR B 59 O HIS B 72 SHEET 4 AA6 6 LYS B 180 VAL B 190 -1 O LEU B 183 N VAL B 60 SHEET 5 AA6 6 SER B 159 GLY B 168 -1 N TYR B 161 O SER B 188 SHEET 6 AA6 6 GLU B 93 PHE B 95 -1 N LEU B 94 O PHE B 166 SHEET 1 AA7 7 GLY B 67 TRP B 68 0 SHEET 2 AA7 7 HIS B 56 SER B 63 -1 N SER B 63 O GLY B 67 SHEET 3 AA7 7 LYS B 180 VAL B 190 -1 O LEU B 183 N VAL B 60 SHEET 4 AA7 7 SER B 159 GLY B 168 -1 N TYR B 161 O SER B 188 SHEET 5 AA7 7 LEU B 98 ARG B 102 -1 N LEU B 98 O ILE B 162 SHEET 6 AA7 7 ILE B 108 PHE B 111 -1 O ARG B 109 N PHE B 101 SHEET 7 AA7 7 THR B 382 VAL B 384 -1 O ILE B 383 N LEU B 110 SHEET 1 AA8 8 LYS B 305 GLU B 308 0 SHEET 2 AA8 8 GLU B 274 THR B 278 1 N LEU B 276 O LYS B 305 SHEET 3 AA8 8 MET B 261 ILE B 268 -1 N LEU B 265 O ALA B 277 SHEET 4 AA8 8 GLN B 254 VAL B 258 -1 N VAL B 258 O MET B 261 SHEET 5 AA8 8 GLN B 244 TYR B 249 -1 N TYR B 249 O GLN B 254 SHEET 6 AA8 8 VAL B 202 TRP B 205 1 N TRP B 205 O LEU B 246 SHEET 7 AA8 8 VAL B 336 TYR B 345 1 O LEU B 344 N LEU B 204 SHEET 8 AA8 8 GLU B 348 HIS B 351 -1 O ILE B 350 N ILE B 343 SHEET 1 AA9 6 LYS B 305 GLU B 308 0 SHEET 2 AA9 6 GLU B 274 THR B 278 1 N LEU B 276 O LYS B 305 SHEET 3 AA9 6 MET B 261 ILE B 268 -1 N LEU B 265 O ALA B 277 SHEET 4 AA9 6 VAL B 325 GLY B 332 -1 O GLU B 327 N TYR B 266 SHEET 5 AA9 6 VAL B 336 TYR B 345 -1 O VAL B 336 N GLY B 332 SHEET 6 AA9 6 GLU B 348 HIS B 351 -1 O ILE B 350 N ILE B 343 SSBOND 1 CYS A 335 CYS A 338 1555 1555 2.03 SSBOND 2 CYS B 335 CYS B 338 1555 1555 1.99 LINK NZ LYS A 222 C4A PLP A 402 1555 1555 1.29 LINK NZ LYS B 222 C4A PLP B 402 1555 1555 1.29 LINK MG MG A 403 O HOH A 572 1555 1555 2.09 LINK MG MG A 403 O HOH A 594 1555 1555 2.05 LINK MG MG A 403 O HOH A 597 1555 3454 2.22 LINK MG MG A 403 O HOH A 601 1555 1555 2.06 LINK MG MG A 403 O HOH A 798 1555 1555 2.09 LINK MG MG A 403 O HOH A 885 1555 3454 2.20 LINK OD2 ASP B 133 MG MG B 403 1555 1555 1.95 LINK MG MG B 403 O HOH B 511 1555 1555 2.01 LINK MG MG B 403 O HOH B 519 1555 1555 1.99 LINK MG MG B 403 O HOH B 535 1555 4455 2.09 LINK MG MG B 403 O HOH B 578 1555 4455 2.13 LINK MG MG B 403 O HOH B 602 1555 4455 2.10 CISPEP 1 GLY A 358 PRO A 359 0 1.01 CISPEP 2 GLY B 358 PRO B 359 0 0.48 CRYST1 66.425 103.001 109.432 90.00 90.00 90.00 P 21 21 21 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 0.015055 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009709 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009138 0.00000