HEADER TRANSFERASE/INHIBITOR 19-AUG-21 7RWH TITLE CRYSTAL STRUCTURE OF HUMAN METHIONINE ADENOSYLTRANSFERASE 2A (MAT2A) TITLE 2 IN COMPLEX WITH SAM AND ALLOSTERIC INHIBITOR AGI-41998 COMPND MOL_ID: 1; COMPND 2 MOLECULE: S-ADENOSYLMETHIONINE SYNTHASE ISOFORM TYPE-2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ADOMET SYNTHASE 2,METHIONINE ADENOSYLTRANSFERASE 2,MAT 2, COMPND 5 METHIONINE ADENOSYLTRANSFERASE II,MAT-II; COMPND 6 EC: 2.5.1.6; 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: MAT2A, AMS2, MATA2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS METHIONINE ADENOSYLTRANSFERASE, SAM, ALLOSTERIC INHIBITOR, KEYWDS 2 TRANSFERASE, TRANSFERASE-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR L.JIN,A.K.PADYANA REVDAT 4 18-OCT-23 7RWH 1 REMARK REVDAT 3 06-APR-22 7RWH 1 JRNL REVDAT 2 30-MAR-22 7RWH 1 JRNL REVDAT 1 23-MAR-22 7RWH 0 JRNL AUTH M.LI,Z.KONTEATIS,N.NAGARAJA,Y.CHEN,S.ZHOU,G.MA,S.GROSS, JRNL AUTH 2 K.MARJON,M.L.HYER,E.MANDLEY,M.LEIN,A.K.PADYANA,L.JIN,S.TONG, JRNL AUTH 3 R.PETERS,J.MURTIE,J.TRAVINS,M.MEDEIROS,P.LIU,V.FRANK, JRNL AUTH 4 E.T.JUDD,S.A.BILLER,K.M.MARKS,Z.SUI,S.K.REZNIK JRNL TITL LEVERAGING STRUCTURE-BASED DRUG DESIGN TO IDENTIFY JRNL TITL 2 NEXT-GENERATION MAT2A INHIBITORS, INCLUDING BRAIN-PENETRANT JRNL TITL 3 AND PERIPHERALLY EFFICACIOUS LEADS. JRNL REF J.MED.CHEM. V. 65 4600 2022 JRNL REFN ISSN 0022-2623 JRNL PMID 35293760 JRNL DOI 10.1021/ACS.JMEDCHEM.1C01595 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Z.KONTEATIS,J.TRAVINS REMARK 1 TITL DISCOVERY OF AG-270, A FIRST-IN-CLASS ORAL MAT2A INHIBITOR REMARK 1 TITL 2 DISCOVERY OF AG-270, A FIRST-IN-CLASS ORAL MAT2A INHIBITOR REMARK 1 REF J.MED.CHEM. V. 64 4430 2021 REMARK 1 REFN ISSN 0022-2623 REMARK 1 PMID 33829783 REMARK 1 DOI 10.1021/ACS.JMEDCHEM.0C01895 REMARK 2 REMARK 2 RESOLUTION. 1.17 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.17 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.95 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.2 REMARK 3 NUMBER OF REFLECTIONS : 116849 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.115 REMARK 3 R VALUE (WORKING SET) : 0.114 REMARK 3 FREE R VALUE : 0.134 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.910 REMARK 3 FREE R VALUE TEST SET COUNT : 5743 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 35.9500 - 3.6300 1.00 4263 197 0.1212 0.1335 REMARK 3 2 3.6300 - 2.8900 1.00 4107 221 0.1030 0.1286 REMARK 3 3 2.8800 - 2.5200 1.00 4054 226 0.1031 0.1333 REMARK 3 4 2.5200 - 2.2900 1.00 4039 205 0.0974 0.1215 REMARK 3 5 2.2900 - 2.1300 1.00 4089 175 0.0984 0.1123 REMARK 3 6 2.1300 - 2.0000 1.00 4026 229 0.0980 0.1167 REMARK 3 7 2.0000 - 1.9000 1.00 4014 223 0.1012 0.1273 REMARK 3 8 1.9000 - 1.8200 1.00 4022 209 0.1057 0.1245 REMARK 3 9 1.8200 - 1.7500 1.00 4017 210 0.1074 0.1140 REMARK 3 10 1.7500 - 1.6900 1.00 4016 197 0.1072 0.1343 REMARK 3 11 1.6900 - 1.6300 1.00 4019 206 0.1092 0.1231 REMARK 3 12 1.6300 - 1.5900 1.00 3975 205 0.1063 0.1355 REMARK 3 13 1.5900 - 1.5500 1.00 4013 220 0.1076 0.1317 REMARK 3 14 1.5500 - 1.5100 1.00 4020 198 0.1094 0.1198 REMARK 3 15 1.5100 - 1.4700 1.00 3958 207 0.1126 0.1269 REMARK 3 16 1.4700 - 1.4400 1.00 4030 197 0.1198 0.1377 REMARK 3 17 1.4400 - 1.4100 1.00 3981 231 0.1218 0.1411 REMARK 3 18 1.4100 - 1.3900 1.00 3973 203 0.1262 0.1458 REMARK 3 19 1.3900 - 1.3600 1.00 3982 228 0.1287 0.1454 REMARK 3 20 1.3600 - 1.3400 1.00 3996 203 0.1317 0.1320 REMARK 3 21 1.3400 - 1.3200 1.00 3974 206 0.1274 0.1522 REMARK 3 22 1.3200 - 1.3000 0.99 3939 212 0.1375 0.1653 REMARK 3 23 1.3000 - 1.2800 0.97 3887 188 0.1493 0.1651 REMARK 3 24 1.2800 - 1.2600 0.93 3724 172 0.1564 0.1664 REMARK 3 25 1.2600 - 1.2400 0.86 3439 184 0.1628 0.1955 REMARK 3 26 1.2400 - 1.2300 0.78 3088 166 0.1683 0.1908 REMARK 3 27 1.2300 - 1.2100 0.70 2741 154 0.1762 0.2056 REMARK 3 28 1.2100 - 1.2000 0.60 2391 123 0.1910 0.2220 REMARK 3 29 1.2000 - 1.1800 0.47 1906 87 0.2039 0.2195 REMARK 3 30 1.1800 - 1.1700 0.36 1423 61 0.2185 0.2421 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.074 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 13.152 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.25 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.78 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.010 3362 REMARK 3 ANGLE : 1.217 4571 REMARK 3 CHIRALITY : 0.098 492 REMARK 3 PLANARITY : 0.010 598 REMARK 3 DIHEDRAL : 19.135 1278 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 11 THROUGH 78 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.6730 6.1845 -19.1968 REMARK 3 T TENSOR REMARK 3 T11: 0.0666 T22: 0.0649 REMARK 3 T33: 0.0766 T12: -0.0045 REMARK 3 T13: 0.0018 T23: -0.0056 REMARK 3 L TENSOR REMARK 3 L11: 0.4476 L22: 0.4188 REMARK 3 L33: 0.6605 L12: -0.2226 REMARK 3 L13: 0.2018 L23: -0.1500 REMARK 3 S TENSOR REMARK 3 S11: -0.0292 S12: -0.0096 S13: 0.0130 REMARK 3 S21: 0.0270 S22: 0.0163 S23: -0.0246 REMARK 3 S31: -0.0203 S32: 0.0208 S33: 0.0118 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 79 THROUGH 104 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.1826 15.9438 -5.5331 REMARK 3 T TENSOR REMARK 3 T11: 0.0818 T22: 0.0931 REMARK 3 T33: 0.0729 T12: -0.0131 REMARK 3 T13: -0.0075 T23: -0.0032 REMARK 3 L TENSOR REMARK 3 L11: 1.5188 L22: 4.0062 REMARK 3 L33: 1.7843 L12: -1.5946 REMARK 3 L13: 0.0856 L23: -0.2558 REMARK 3 S TENSOR REMARK 3 S11: -0.0475 S12: -0.0247 S13: 0.0916 REMARK 3 S21: 0.1015 S22: 0.0292 S23: -0.0783 REMARK 3 S31: -0.0556 S32: 0.1062 S33: 0.0285 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 105 THROUGH 341 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.0285 9.7492 -28.8486 REMARK 3 T TENSOR REMARK 3 T11: 0.0720 T22: 0.0726 REMARK 3 T33: 0.0765 T12: -0.0055 REMARK 3 T13: -0.0011 T23: 0.0019 REMARK 3 L TENSOR REMARK 3 L11: 0.1889 L22: 0.2699 REMARK 3 L33: 0.1801 L12: -0.0900 REMARK 3 L13: -0.0142 L23: -0.0101 REMARK 3 S TENSOR REMARK 3 S11: -0.0020 S12: 0.0067 S13: 0.0227 REMARK 3 S21: -0.0121 S22: 0.0032 S23: -0.0084 REMARK 3 S31: -0.0177 S32: -0.0022 S33: -0.0025 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 342 THROUGH 364 ) REMARK 3 ORIGIN FOR THE GROUP (A): 21.3214 -5.6556 -39.2070 REMARK 3 T TENSOR REMARK 3 T11: 0.1082 T22: 0.0966 REMARK 3 T33: 0.1112 T12: -0.0019 REMARK 3 T13: 0.0136 T23: 0.0057 REMARK 3 L TENSOR REMARK 3 L11: 1.5742 L22: 0.5667 REMARK 3 L33: 2.9548 L12: -0.6845 REMARK 3 L13: 0.9746 L23: -0.8545 REMARK 3 S TENSOR REMARK 3 S11: 0.0874 S12: 0.1805 S13: -0.0596 REMARK 3 S21: -0.1196 S22: -0.0070 S23: -0.0270 REMARK 3 S31: 0.2571 S32: 0.1636 S33: -0.1035 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 365 THROUGH 395 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.8414 7.8815 -28.8093 REMARK 3 T TENSOR REMARK 3 T11: 0.0774 T22: 0.0734 REMARK 3 T33: 0.1014 T12: -0.0157 REMARK 3 T13: -0.0015 T23: -0.0012 REMARK 3 L TENSOR REMARK 3 L11: 0.8303 L22: 0.9220 REMARK 3 L33: 1.3168 L12: 0.1443 REMARK 3 L13: 0.4838 L23: -0.3647 REMARK 3 S TENSOR REMARK 3 S11: -0.0544 S12: 0.0188 S13: 0.0734 REMARK 3 S21: 0.0000 S22: 0.0389 S23: -0.1234 REMARK 3 S31: -0.0772 S32: 0.1015 S33: -0.0151 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7RWH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-AUG-21. REMARK 100 THE DEPOSITION ID IS D_1000259130. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUL-19 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 : APS REMARK 200 BEAMLINE : 21-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1271 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 116890 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.170 REMARK 200 RESOLUTION RANGE LOW (A) : 36.630 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.3 REMARK 200 DATA REDUNDANCY : 11.60 REMARK 200 R MERGE (I) : 0.11400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.17 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.20 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.67500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 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: 2P02 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M LICL, 0.1 M TRIS PH 8.0, 18%-20% REMARK 280 PEG6000, 10% ETHYLENE GLYCOL, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-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 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 34.28000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 47.05500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 58.34500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 34.28000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 47.05500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 58.34500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 34.28000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 47.05500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 58.34500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 34.28000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 47.05500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 58.34500 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: 10170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -78.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 MG MG A 412 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 601 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 624 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 650 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 861 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 897 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 997 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 ASN A 2 REMARK 465 GLY A 3 REMARK 465 GLN A 4 REMARK 465 LEU A 5 REMARK 465 ASN A 6 REMARK 465 GLY A 7 REMARK 465 PHE A 8 REMARK 465 HIS A 9 REMARK 465 GLU A 10 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 HG1 THR A 172 O HOH A 502 1.40 REMARK 500 O HOH A 687 O HOH A 694 1.87 REMARK 500 O HOH A 561 O HOH A 888 1.88 REMARK 500 O HOH A 868 O HOH A 896 1.89 REMARK 500 O HOH A 556 O HOH A 782 1.93 REMARK 500 O HOH A 833 O HOH A 879 1.93 REMARK 500 OE1 GLU A 347 O HOH A 501 1.94 REMARK 500 OG1 THR A 172 O HOH A 502 1.94 REMARK 500 O HOH A 833 O HOH A 857 1.96 REMARK 500 OE2 GLU A 14 O HOH A 503 1.98 REMARK 500 O HOH A 584 O HOH A 749 1.99 REMARK 500 O HOH A 620 O HOH A 836 2.00 REMARK 500 O HOH A 671 O HOH A 868 2.07 REMARK 500 O HOH A 579 O HOH A 787 2.08 REMARK 500 O HOH A 823 O HOH A 933 2.08 REMARK 500 O1 EDO A 403 O HOH A 504 2.09 REMARK 500 O HOH A 637 O HOH A 769 2.15 REMARK 500 O HOH A 695 O HOH A 893 2.16 REMARK 500 O HOH A 518 O HOH A 732 2.19 REMARK 500 O HOH A 863 O HOH A 877 2.19 REMARK 500 O HOH A 856 O HOH A 922 2.19 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 199 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 PHE A 250 CB - CG - CD2 ANGL. DEV. = -4.7 DEGREES REMARK 500 PHE A 250 CB - CG - CD1 ANGL. DEV. = 5.0 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 VAL A 226 -67.36 -109.09 REMARK 500 THR A 270 -101.94 -118.70 REMARK 500 ARG A 292 -61.70 -90.77 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 A1029 DISTANCE = 6.69 ANGSTROMS REMARK 525 HOH A1030 DISTANCE = 6.92 ANGSTROMS REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 1PE A 408 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 412 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 608 O REMARK 620 2 HOH A 864 O 140.2 REMARK 620 3 HOH A 864 O 99.4 87.1 REMARK 620 N 1 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7KCC RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH AGI-270 REMARK 900 RELATED ID: 7RW5 RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH AGI-0034515 REMARK 900 RELATED ID: 7RW7 RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH AGI-0039899 REMARK 900 RELATED ID: 7RWG RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH AGI-0043192 DBREF 7RWH A 1 395 UNP P31153 METK2_HUMAN 1 395 SEQADV 7RWH SER A 0 UNP P31153 EXPRESSION TAG SEQRES 1 A 396 SER MET ASN GLY GLN LEU ASN GLY PHE HIS GLU ALA PHE SEQRES 2 A 396 ILE GLU GLU GLY THR PHE LEU PHE THR SER GLU SER VAL SEQRES 3 A 396 GLY GLU GLY HIS PRO ASP LYS ILE CYS ASP GLN ILE SER SEQRES 4 A 396 ASP ALA VAL LEU ASP ALA HIS LEU GLN GLN ASP PRO ASP SEQRES 5 A 396 ALA LYS VAL ALA CYS GLU THR VAL ALA LYS THR GLY MET SEQRES 6 A 396 ILE LEU LEU ALA GLY GLU ILE THR SER ARG ALA ALA VAL SEQRES 7 A 396 ASP TYR GLN LYS VAL VAL ARG GLU ALA VAL LYS HIS ILE SEQRES 8 A 396 GLY TYR ASP ASP SER SER LYS GLY PHE ASP TYR LYS THR SEQRES 9 A 396 CYS ASN VAL LEU VAL ALA LEU GLU GLN GLN SER PRO ASP SEQRES 10 A 396 ILE ALA GLN GLY VAL HIS LEU ASP ARG ASN GLU GLU ASP SEQRES 11 A 396 ILE GLY ALA GLY ASP GLN GLY LEU MET PHE GLY TYR ALA SEQRES 12 A 396 THR ASP GLU THR GLU GLU CYS MET PRO LEU THR ILE VAL SEQRES 13 A 396 LEU ALA HIS LYS LEU ASN ALA LYS LEU ALA GLU LEU ARG SEQRES 14 A 396 ARG ASN GLY THR LEU PRO TRP LEU ARG PRO ASP SER LYS SEQRES 15 A 396 THR GLN VAL THR VAL GLN TYR MET GLN ASP ARG GLY ALA SEQRES 16 A 396 VAL LEU PRO ILE ARG VAL HIS THR ILE VAL ILE SER VAL SEQRES 17 A 396 GLN HIS ASP GLU GLU VAL CYS LEU ASP GLU MET ARG ASP SEQRES 18 A 396 ALA LEU LYS GLU LYS VAL ILE LYS ALA VAL VAL PRO ALA SEQRES 19 A 396 LYS TYR LEU ASP GLU ASP THR ILE TYR HIS LEU GLN PRO SEQRES 20 A 396 SER GLY ARG PHE VAL ILE GLY GLY PRO GLN GLY ASP ALA SEQRES 21 A 396 GLY LEU THR GLY ARG LYS ILE ILE VAL ASP THR TYR GLY SEQRES 22 A 396 GLY TRP GLY ALA HIS GLY GLY GLY ALA PHE SER GLY LYS SEQRES 23 A 396 ASP TYR THR LYS VAL ASP ARG SER ALA ALA TYR ALA ALA SEQRES 24 A 396 ARG TRP VAL ALA LYS SER LEU VAL LYS GLY GLY LEU CYS SEQRES 25 A 396 ARG ARG VAL LEU VAL GLN VAL SER TYR ALA ILE GLY VAL SEQRES 26 A 396 SER HIS PRO LEU SER ILE SER ILE PHE HIS TYR GLY THR SEQRES 27 A 396 SER GLN LYS SER GLU ARG GLU LEU LEU GLU ILE VAL LYS SEQRES 28 A 396 LYS ASN PHE ASP LEU ARG PRO GLY VAL ILE VAL ARG ASP SEQRES 29 A 396 LEU ASP LEU LYS LYS PRO ILE TYR GLN ARG THR ALA ALA SEQRES 30 A 396 TYR GLY HIS PHE GLY ARG ASP SER PHE PRO TRP GLU VAL SEQRES 31 A 396 PRO LYS LYS LEU LYS TYR HET SAM A 401 46 HET 7UI A 402 48 HET EDO A 403 10 HET EDO A 404 20 HET EDO A 405 10 HET EDO A 406 10 HET GOL A 407 14 HET 1PE A 408 35 HET CL A 409 1 HET MG A 410 1 HET MG A 411 1 HET MG A 412 1 HETNAM SAM S-ADENOSYLMETHIONINE HETNAM 7UI 8-(4-BROMOPHENYL)-6-(4-METHOXYPHENYL)-2-[2,2,2- HETNAM 2 7UI TRIS(FLUORANYL)ETHYLAMINO]PYRIDO[4,3-D]PYRIMIDIN-7-OL HETNAM EDO 1,2-ETHANEDIOL HETNAM GOL GLYCEROL HETNAM 1PE PENTAETHYLENE GLYCOL HETNAM CL CHLORIDE ION HETNAM MG MAGNESIUM ION HETSYN EDO ETHYLENE GLYCOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN 1PE PEG400 FORMUL 2 SAM C15 H22 N6 O5 S FORMUL 3 7UI C22 H16 BR F3 N4 O2 FORMUL 4 EDO 4(C2 H6 O2) FORMUL 8 GOL C3 H8 O3 FORMUL 9 1PE C10 H22 O6 FORMUL 10 CL CL 1- FORMUL 11 MG 3(MG 2+) FORMUL 14 HOH *530(H2 O) HELIX 1 AA1 HIS A 29 ASP A 49 1 21 HELIX 2 AA2 ASP A 78 GLY A 91 1 14 HELIX 3 AA3 SER A 95 GLY A 98 5 4 HELIX 4 AA4 SER A 114 HIS A 122 1 9 HELIX 5 AA5 ASN A 126 ILE A 130 5 5 HELIX 6 AA6 PRO A 151 ASN A 170 1 20 HELIX 7 AA7 CYS A 214 LYS A 225 1 12 HELIX 8 AA8 VAL A 226 VAL A 231 1 6 HELIX 9 AA9 PRO A 232 LEU A 236 5 5 HELIX 10 AB1 GLY A 253 GLY A 257 5 5 HELIX 11 AB2 LYS A 289 GLY A 308 1 20 HELIX 12 AB3 SER A 341 PHE A 353 1 13 HELIX 13 AB4 ARG A 356 ASP A 365 1 10 HELIX 14 AB5 ILE A 370 ALA A 375 5 6 HELIX 15 AB6 PHE A 385 VAL A 389 5 5 SHEET 1 AA1 4 THR A 17 VAL A 25 0 SHEET 2 AA1 4 LEU A 176 ASP A 191 -1 O TYR A 188 N PHE A 18 SHEET 3 AA1 4 ALA A 194 HIS A 209 -1 O ILE A 198 N GLN A 187 SHEET 4 AA1 4 ILE A 241 LEU A 244 1 O HIS A 243 N ILE A 203 SHEET 1 AA2 4 ASN A 105 GLU A 111 0 SHEET 2 AA2 4 MET A 64 THR A 72 1 N LEU A 67 O ALA A 109 SHEET 3 AA2 4 LYS A 53 LYS A 61 -1 N LYS A 61 O MET A 64 SHEET 4 AA2 4 GLY A 260 LEU A 261 -1 O GLY A 260 N ALA A 60 SHEET 1 AA3 2 ASP A 93 ASP A 94 0 SHEET 2 AA3 2 PHE A 99 ASP A 100 -1 O PHE A 99 N ASP A 94 SHEET 1 AA4 3 GLY A 136 THR A 143 0 SHEET 2 AA4 3 ARG A 313 TYR A 320 -1 O VAL A 318 N MET A 138 SHEET 3 AA4 3 SER A 329 PHE A 333 -1 O PHE A 333 N LEU A 315 LINK MG MG A 411 O HOH A 608 1555 1555 2.86 LINK MG MG A 412 O HOH A 608 1555 2555 2.96 LINK MG MG A 412 O HOH A 864 1555 1555 2.97 LINK MG MG A 412 O HOH A 864 1555 2555 2.90 CRYST1 68.560 94.110 116.690 90.00 90.00 90.00 I 2 2 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.014586 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010626 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008570 0.00000