HEADER TRANSFERASE/INHIBITOR 05-OCT-20 7KCE TITLE CRYSTAL STRUCTURE OF HUMAN METHIONINE ADENOSYLTRANSFERASE 2A (MAT2A) TITLE 2 IN COMPLEX WITH SAM AND ALLOSTERIC INHIBITOR COMPOUND 2 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, S-ADENOSYLMETHIONINE SYNTHASE ISOFORM KEYWDS 2 TYPE-2, SAM, ALLOSTERIC INHIBITOR, TRANSFERASE, TRANSFERASE- KEYWDS 3 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.PADYANA,L.JIN REVDAT 3 18-OCT-23 7KCE 1 REMARK REVDAT 2 05-MAY-21 7KCE 1 JRNL REVDAT 1 21-APR-21 7KCE 0 JRNL AUTH Z.KONTEATIS,J.TRAVINS,S.GROSS,K.MARJON,A.BARNETT,E.MANDLEY, JRNL AUTH 2 B.NICOLAY,R.NAGARAJA,Y.CHEN,Y.SUN,Z.LIU,J.YU,Z.YE,F.JIANG, JRNL AUTH 3 W.WEI,C.FANG,Y.GAO,P.KALEV,M.L.HYER,B.DELABARRE,L.JIN, JRNL AUTH 4 A.K.PADYANA,L.DANG,J.MURTIE,S.A.BILLER,Z.SUI,K.M.MARKS JRNL TITL DISCOVERY OF AG-270, A FIRST-IN-CLASS ORAL MAT2A INHIBITOR JRNL TITL 2 FOR THE TREATMENT OF TUMORS WITH HOMOZYGOUS MTAP DELETION. JRNL REF J.MED.CHEM. V. 64 4430 2021 JRNL REFN ISSN 0022-2623 JRNL PMID 33829783 JRNL DOI 10.1021/ACS.JMEDCHEM.0C01895 REMARK 2 REMARK 2 RESOLUTION. 1.14 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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) : 1.14 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.37 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 131328 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.144 REMARK 3 R VALUE (WORKING SET) : 0.144 REMARK 3 FREE R VALUE : 0.159 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 6614 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 29.3700 - 3.5500 0.85 3890 200 0.1315 0.1439 REMARK 3 2 3.5500 - 2.8200 0.98 4277 243 0.1194 0.1403 REMARK 3 3 2.8100 - 2.4600 0.98 4280 215 0.1207 0.1360 REMARK 3 4 2.4600 - 2.2300 0.96 4102 241 0.1212 0.1482 REMARK 3 5 2.2300 - 2.0700 0.97 4147 248 0.1204 0.1302 REMARK 3 6 2.0700 - 1.9500 0.96 4106 237 0.1197 0.1380 REMARK 3 7 1.9500 - 1.8500 0.95 4078 219 0.1397 0.1487 REMARK 3 8 1.8500 - 1.7700 0.98 4233 221 0.1306 0.1417 REMARK 3 9 1.7700 - 1.7100 0.99 4225 209 0.1339 0.1483 REMARK 3 10 1.7100 - 1.6500 0.99 4240 228 0.1326 0.1539 REMARK 3 11 1.6500 - 1.6000 0.99 4248 243 0.1318 0.1549 REMARK 3 12 1.6000 - 1.5500 0.99 4239 209 0.1349 0.1531 REMARK 3 13 1.5500 - 1.5100 0.99 4240 211 0.1452 0.1650 REMARK 3 14 1.5100 - 1.4700 0.99 4196 234 0.1578 0.1598 REMARK 3 15 1.4700 - 1.4400 0.99 4262 214 0.1508 0.1616 REMARK 3 16 1.4400 - 1.4100 0.99 4290 200 0.1704 0.1862 REMARK 3 17 1.4100 - 1.3800 0.99 4231 224 0.1667 0.1898 REMARK 3 18 1.3800 - 1.3500 0.99 4217 222 0.1746 0.1915 REMARK 3 19 1.3500 - 1.3300 0.99 4233 202 0.1767 0.1847 REMARK 3 20 1.3300 - 1.3100 0.99 4205 220 0.1884 0.2007 REMARK 3 21 1.3100 - 1.2900 0.99 4207 258 0.1933 0.2052 REMARK 3 22 1.2900 - 1.2700 0.99 4215 207 0.1965 0.2059 REMARK 3 23 1.2700 - 1.2500 0.99 4193 235 0.2013 0.2251 REMARK 3 24 1.2500 - 1.2300 0.99 4174 217 0.2073 0.2433 REMARK 3 25 1.2300 - 1.2100 0.99 4217 219 0.2172 0.2044 REMARK 3 26 1.2100 - 1.2000 0.99 4185 234 0.2231 0.2185 REMARK 3 27 1.2000 - 1.1800 0.98 4183 219 0.2114 0.2177 REMARK 3 28 1.1800 - 1.1700 0.95 4042 204 0.2166 0.2271 REMARK 3 29 1.1700 - 1.1500 0.90 3817 178 0.2262 0.2275 REMARK 3 30 1.1500 - 1.1400 0.84 3542 203 0.2245 0.2279 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) : 0.071 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.343 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.44 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.35 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 : 0.011 3306 REMARK 3 ANGLE : 1.198 4516 REMARK 3 CHIRALITY : 0.097 494 REMARK 3 PLANARITY : 0.010 601 REMARK 3 DIHEDRAL : 17.220 1296 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 16 THROUGH 78 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.2639 5.1881 -15.7804 REMARK 3 T TENSOR REMARK 3 T11: 0.0636 T22: 0.0717 REMARK 3 T33: 0.0687 T12: -0.0004 REMARK 3 T13: 0.0004 T23: -0.0078 REMARK 3 L TENSOR REMARK 3 L11: 0.4225 L22: 0.4899 REMARK 3 L33: 0.4624 L12: -0.1496 REMARK 3 L13: 0.1271 L23: -0.1710 REMARK 3 S TENSOR REMARK 3 S11: -0.0136 S12: 0.0069 S13: 0.0142 REMARK 3 S21: 0.0236 S22: 0.0104 S23: -0.0511 REMARK 3 S31: -0.0045 S32: 0.0680 S33: 0.0057 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 79 THROUGH 104 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.2695 16.0215 -5.5662 REMARK 3 T TENSOR REMARK 3 T11: 0.0912 T22: 0.1016 REMARK 3 T33: 0.0829 T12: -0.0114 REMARK 3 T13: -0.0077 T23: -0.0015 REMARK 3 L TENSOR REMARK 3 L11: 0.8109 L22: 1.9527 REMARK 3 L33: 1.2593 L12: -0.2926 REMARK 3 L13: -0.0222 L23: 0.0832 REMARK 3 S TENSOR REMARK 3 S11: -0.0358 S12: -0.0223 S13: 0.1204 REMARK 3 S21: 0.0902 S22: 0.0280 S23: -0.0775 REMARK 3 S31: -0.0828 S32: 0.1716 S33: 0.0151 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 105 THROUGH 169 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.2292 2.0849 -24.1854 REMARK 3 T TENSOR REMARK 3 T11: 0.0564 T22: 0.0862 REMARK 3 T33: 0.0867 T12: -0.0099 REMARK 3 T13: 0.0013 T23: 0.0008 REMARK 3 L TENSOR REMARK 3 L11: 0.1613 L22: 0.6044 REMARK 3 L33: 0.3042 L12: -0.1622 REMARK 3 L13: 0.0055 L23: -0.0880 REMARK 3 S TENSOR REMARK 3 S11: -0.0047 S12: 0.0133 S13: 0.0231 REMARK 3 S21: -0.0279 S22: 0.0010 S23: -0.0675 REMARK 3 S31: 0.0101 S32: 0.0474 S33: 0.0062 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 170 THROUGH 244 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.8629 23.8753 -30.8534 REMARK 3 T TENSOR REMARK 3 T11: 0.0748 T22: 0.0770 REMARK 3 T33: 0.0943 T12: -0.0039 REMARK 3 T13: -0.0005 T23: 0.0231 REMARK 3 L TENSOR REMARK 3 L11: 0.7234 L22: 1.0168 REMARK 3 L33: 1.0036 L12: -0.0747 REMARK 3 L13: 0.1421 L23: 0.2100 REMARK 3 S TENSOR REMARK 3 S11: 0.0017 S12: 0.0850 S13: 0.0954 REMARK 3 S21: -0.1154 S22: 0.0203 S23: 0.0095 REMARK 3 S31: -0.1105 S32: 0.0227 S33: -0.0170 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 245 THROUGH 341 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.3188 1.8158 -31.6603 REMARK 3 T TENSOR REMARK 3 T11: 0.0753 T22: 0.0736 REMARK 3 T33: 0.0645 T12: -0.0087 REMARK 3 T13: 0.0027 T23: 0.0033 REMARK 3 L TENSOR REMARK 3 L11: 0.3805 L22: 0.5586 REMARK 3 L33: 0.2419 L12: -0.2130 REMARK 3 L13: -0.0423 L23: 0.0864 REMARK 3 S TENSOR REMARK 3 S11: 0.0059 S12: 0.0562 S13: 0.0022 REMARK 3 S21: -0.0989 S22: -0.0016 S23: -0.0196 REMARK 3 S31: -0.0174 S32: 0.0146 S33: -0.0052 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 342 THROUGH 364 ) REMARK 3 ORIGIN FOR THE GROUP (A): 21.4617 -5.2746 -38.7044 REMARK 3 T TENSOR REMARK 3 T11: 0.1713 T22: 0.1117 REMARK 3 T33: 0.1112 T12: 0.0123 REMARK 3 T13: 0.0404 T23: -0.0030 REMARK 3 L TENSOR REMARK 3 L11: 0.7944 L22: 1.0863 REMARK 3 L33: 1.2329 L12: -0.3939 REMARK 3 L13: 0.0103 L23: -0.7970 REMARK 3 S TENSOR REMARK 3 S11: 0.0312 S12: 0.2084 S13: -0.0532 REMARK 3 S21: -0.3897 S22: -0.0683 S23: -0.1737 REMARK 3 S31: 0.2649 S32: 0.1264 S33: 0.0134 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 365 THROUGH 395 ) REMARK 3 ORIGIN FOR THE GROUP (A): 19.0071 7.7099 -30.0159 REMARK 3 T TENSOR REMARK 3 T11: 0.0929 T22: 0.0917 REMARK 3 T33: 0.1111 T12: -0.0191 REMARK 3 T13: 0.0133 T23: -0.0009 REMARK 3 L TENSOR REMARK 3 L11: 1.0843 L22: 0.7509 REMARK 3 L33: 1.0111 L12: -0.0258 REMARK 3 L13: 0.0109 L23: -0.4549 REMARK 3 S TENSOR REMARK 3 S11: -0.0321 S12: 0.0687 S13: 0.1149 REMARK 3 S21: -0.0840 S22: 0.0177 S23: -0.1635 REMARK 3 S31: -0.0490 S32: 0.1153 S33: -0.0021 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 7KCE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-OCT-20. REMARK 100 THE DEPOSITION ID IS D_1000252243. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-MAR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.8 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-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 131343 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.140 REMARK 200 RESOLUTION RANGE LOW (A) : 29.370 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.14 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.17 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.48300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: 2P02 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M LITHIUM CHLORIDE, 0.1M TRIS PH REMARK 280 7.8, 20% PEG 6000, 10% ETHYLENE GLYCOL, VAPOR DIFFUSION, HANGING REMARK 280 DROP, 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 33.98500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 47.12000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 58.40500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 33.98500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 47.12000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 58.40500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 33.98500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 47.12000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 58.40500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 33.98500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 47.12000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 58.40500 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: 6890 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24640 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -51.0 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 HOH A 512 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 660 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 874 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 907 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1010 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 465 ALA A 11 REMARK 465 PHE A 12 REMARK 465 ILE A 13 REMARK 465 GLU A 14 REMARK 465 GLU A 15 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 HZ1 LYS A 307 O HOH A 501 1.58 REMARK 500 O HOH A 639 O HOH A 645 1.71 REMARK 500 O HOH A 639 O HOH A 681 1.79 REMARK 500 O HOH A 546 O HOH A 864 1.94 REMARK 500 O HOH A 869 O HOH A 994 1.96 REMARK 500 O HOH A 612 O HOH A 968 1.97 REMARK 500 O HOH A 516 O HOH A 535 2.00 REMARK 500 O HOH A 502 O HOH A 886 2.01 REMARK 500 O HOH A 821 O HOH A 1008 2.01 REMARK 500 O HOH A 559 O HOH A 666 2.04 REMARK 500 O HOH A 552 O HOH A 830 2.04 REMARK 500 O HOH A 594 O HOH A 909 2.07 REMARK 500 O HOH A 634 O HOH A 683 2.07 REMARK 500 O HOH A 657 O HOH A 903 2.08 REMARK 500 O HOH A 643 O HOH A 645 2.11 REMARK 500 O HOH A 685 O HOH A 869 2.12 REMARK 500 O HOH A 622 O HOH A 894 2.13 REMARK 500 O HOH A 740 O HOH A 774 2.14 REMARK 500 O HOH A 516 O HOH A 959 2.15 REMARK 500 O HOH A 701 O HOH A 811 2.16 REMARK 500 O HOH A 530 O HOH A 779 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 502 O HOH A 517 2555 1.86 REMARK 500 O HOH A 666 O HOH A 968 7554 1.90 REMARK 500 O HOH A 550 O HOH A 934 8454 1.97 REMARK 500 O HOH A 724 O HOH A 870 7554 2.13 REMARK 500 OE1 GLU A 147 O HOH A 833 8554 2.16 REMARK 500 O HOH A 739 O HOH A 972 2555 2.17 REMARK 500 O HOH A 517 O HOH A 886 2555 2.18 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 219 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 PHE A 250 CB - CG - CD2 ANGL. DEV. = -4.8 DEGREES REMARK 500 PHE A 250 CB - CG - CD1 ANGL. DEV. = 4.7 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 LEU A 173 77.50 -119.41 REMARK 500 ASP A 191 80.28 -151.23 REMARK 500 ASP A 191 80.28 -151.54 REMARK 500 VAL A 226 -67.15 -106.99 REMARK 500 THR A 270 -103.07 -120.89 REMARK 500 ARG A 292 -62.47 -91.84 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 A1044 DISTANCE = 6.04 ANGSTROMS REMARK 525 HOH A1045 DISTANCE = 6.25 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue J41 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SAM A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 403 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7KCC RELATED DB: PDB REMARK 900 7KCC CONTAINS THE SAME PROTEIN COMPLEXED WITH AGI-270 REMARK 900 RELATED ID: 7KCF RELATED DB: PDB REMARK 900 7KCF CONTAINS THE SAME PROTEIN COMPLEXED WITH AGI-24512 REMARK 900 RELATED ID: 7KDA RELATED DB: PDB REMARK 900 RELATED ID: 7KDB RELATED DB: PDB DBREF 7KCE A 1 395 UNP P31153 METK2_HUMAN 1 395 SEQADV 7KCE 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 J41 A 401 38 HET SAM A 402 49 HET CL A 403 1 HETNAM J41 5-METHYL-2,3-DIPHENYLPYRAZOLO[1,5-A]PYRIMIDIN-7(4H)-ONE HETNAM SAM S-ADENOSYLMETHIONINE HETNAM CL CHLORIDE ION FORMUL 2 J41 C19 H15 N3 O FORMUL 3 SAM C15 H22 N6 O5 S FORMUL 4 CL CL 1- FORMUL 5 HOH *545(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 53 O THR A 72 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 316 N GLY A 140 SHEET 3 AA4 3 SER A 329 PHE A 333 -1 O PHE A 333 N LEU A 315 SITE 1 AC1 14 PHE A 18 PHE A 20 GLN A 190 GLY A 273 SITE 2 AC1 14 TRP A 274 ARG A 313 LEU A 315 SER A 331 SITE 3 AC1 14 PHE A 333 GLU A 342 HOH A 510 HOH A 518 SITE 4 AC1 14 HOH A 847 HOH A1045 SITE 1 AC2 22 HIS A 29 PRO A 30 ALA A 55 GLU A 70 SITE 2 AC2 22 GLN A 113 ASP A 116 ILE A 117 GLY A 133 SITE 3 AC2 22 ASP A 134 ASP A 179 LYS A 181 SER A 247 SITE 4 AC2 22 ARG A 249 PHE A 250 ASP A 258 LYS A 289 SITE 5 AC2 22 CL A 403 HOH A 613 HOH A 636 HOH A 734 SITE 6 AC2 22 HOH A 735 HOH A 861 SITE 1 AC3 6 HIS A 29 ASP A 134 LYS A 181 LYS A 265 SITE 2 AC3 6 SAM A 402 HOH A 516 CRYST1 67.970 94.240 116.810 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 0.014712 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010611 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008561 0.00000