HEADER TRANSFERASE/INHIBITOR 08-OCT-20 7KDA TITLE CRYSTAL STRUCTURE OF HUMAN METHIONINE ADENOSYLTRANSFERASE 2A (MAT2A) TITLE 2 IN COMPLEX WITH SAM AND ALLOSTERIC INHIBITOR COMPOUND 34 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 A.PADYANA,L.JIN REVDAT 3 18-OCT-23 7KDA 1 REMARK REVDAT 2 05-MAY-21 7KDA 1 JRNL REVDAT 1 21-APR-21 7KDA 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. 1.24 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) : 1.24 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.27 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 105066 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.127 REMARK 3 R VALUE (WORKING SET) : 0.127 REMARK 3 FREE R VALUE : 0.139 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.890 REMARK 3 FREE R VALUE TEST SET COUNT : 5134 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 30.2700 - 3.8600 0.90 3188 182 0.1522 0.1513 REMARK 3 2 3.8600 - 3.0600 0.98 3396 154 0.1214 0.1314 REMARK 3 3 3.0600 - 2.6800 1.00 3417 157 0.1201 0.1363 REMARK 3 4 2.6800 - 2.4300 1.00 3354 197 0.1147 0.1280 REMARK 3 5 2.4300 - 2.2600 1.00 3393 174 0.1150 0.1348 REMARK 3 6 2.2600 - 2.1200 1.00 3358 172 0.1141 0.1258 REMARK 3 7 2.1200 - 2.0200 1.00 3345 178 0.1153 0.1309 REMARK 3 8 2.0200 - 1.9300 1.00 3328 197 0.1168 0.1217 REMARK 3 9 1.9300 - 1.8600 1.00 3364 178 0.1194 0.1355 REMARK 3 10 1.8600 - 1.7900 1.00 3307 177 0.1193 0.1265 REMARK 3 11 1.7900 - 1.7400 1.00 3319 206 0.1186 0.1364 REMARK 3 12 1.7400 - 1.6900 1.00 3345 170 0.1153 0.1288 REMARK 3 13 1.6900 - 1.6400 1.00 3357 168 0.1157 0.1240 REMARK 3 14 1.6400 - 1.6000 1.00 3328 179 0.1190 0.1462 REMARK 3 15 1.6000 - 1.5600 1.00 3317 168 0.1214 0.1319 REMARK 3 16 1.5600 - 1.5300 1.00 3366 138 0.1202 0.1374 REMARK 3 17 1.5300 - 1.5000 1.00 3323 164 0.1247 0.1243 REMARK 3 18 1.5000 - 1.4700 1.00 3335 154 0.1269 0.1441 REMARK 3 19 1.4700 - 1.4500 1.00 3312 182 0.1290 0.1499 REMARK 3 20 1.4500 - 1.4200 1.00 3328 152 0.1366 0.1428 REMARK 3 21 1.4200 - 1.4000 1.00 3356 157 0.1395 0.1733 REMARK 3 22 1.4000 - 1.3800 1.00 3335 168 0.1382 0.1626 REMARK 3 23 1.3800 - 1.3600 1.00 3359 163 0.1413 0.1584 REMARK 3 24 1.3600 - 1.3400 1.00 3294 160 0.1476 0.1401 REMARK 3 25 1.3400 - 1.3200 1.00 3325 175 0.1455 0.1361 REMARK 3 26 1.3200 - 1.3000 1.00 3315 163 0.1516 0.1755 REMARK 3 27 1.3000 - 1.2900 1.00 3307 167 0.1487 0.1610 REMARK 3 28 1.2900 - 1.2700 1.00 3297 191 0.1561 0.1634 REMARK 3 29 1.2700 - 1.2600 1.00 3299 196 0.1620 0.1736 REMARK 3 30 1.2600 - 1.2400 0.98 3265 147 0.1711 0.1851 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) : 0.072 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 11.789 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.14 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.74 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 3221 REMARK 3 ANGLE : 1.167 4391 REMARK 3 CHIRALITY : 0.091 483 REMARK 3 PLANARITY : 0.009 567 REMARK 3 DIHEDRAL : 19.689 1225 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 9 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 15 THROUGH 48 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.0450 9.1947 -22.5828 REMARK 3 T TENSOR REMARK 3 T11: 0.0546 T22: 0.0589 REMARK 3 T33: 0.0568 T12: -0.0033 REMARK 3 T13: 0.0019 T23: -0.0007 REMARK 3 L TENSOR REMARK 3 L11: 1.0616 L22: 0.5360 REMARK 3 L33: 0.6794 L12: -0.3700 REMARK 3 L13: 0.6329 L23: -0.3187 REMARK 3 S TENSOR REMARK 3 S11: -0.0088 S12: 0.0665 S13: 0.0135 REMARK 3 S21: -0.0282 S22: 0.0105 S23: -0.0074 REMARK 3 S31: -0.0249 S32: 0.0729 S33: 0.0384 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 49 THROUGH 78 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.3875 0.5355 -9.1524 REMARK 3 T TENSOR REMARK 3 T11: 0.0908 T22: 0.0953 REMARK 3 T33: 0.0820 T12: 0.0030 REMARK 3 T13: -0.0061 T23: -0.0034 REMARK 3 L TENSOR REMARK 3 L11: 0.3678 L22: 1.2239 REMARK 3 L33: 0.7855 L12: -0.5244 REMARK 3 L13: -0.4935 L23: 0.3923 REMARK 3 S TENSOR REMARK 3 S11: -0.0372 S12: -0.0215 S13: -0.0454 REMARK 3 S21: 0.0441 S22: 0.0135 S23: -0.0073 REMARK 3 S31: -0.0123 S32: 0.0609 S33: 0.0287 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 79 THROUGH 143 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.7209 1.5009 -13.2797 REMARK 3 T TENSOR REMARK 3 T11: 0.0679 T22: 0.0908 REMARK 3 T33: 0.0807 T12: -0.0019 REMARK 3 T13: -0.0032 T23: 0.0009 REMARK 3 L TENSOR REMARK 3 L11: 0.1357 L22: 0.4378 REMARK 3 L33: 0.1950 L12: -0.1029 REMARK 3 L13: -0.0157 L23: 0.0104 REMARK 3 S TENSOR REMARK 3 S11: -0.0237 S12: -0.0253 S13: -0.0007 REMARK 3 S21: 0.0530 S22: 0.0270 S23: -0.0260 REMARK 3 S31: 0.0192 S32: 0.0392 S33: -0.0257 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 144 THROUGH 169 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.3284 18.4827 -31.1656 REMARK 3 T TENSOR REMARK 3 T11: 0.0732 T22: 0.0765 REMARK 3 T33: 0.0888 T12: -0.0113 REMARK 3 T13: 0.0008 T23: 0.0149 REMARK 3 L TENSOR REMARK 3 L11: 0.1293 L22: 2.2042 REMARK 3 L33: 2.9137 L12: -0.2822 REMARK 3 L13: -0.0357 L23: 1.8723 REMARK 3 S TENSOR REMARK 3 S11: 0.0287 S12: -0.0151 S13: 0.0369 REMARK 3 S21: -0.0571 S22: 0.0237 S23: -0.1013 REMARK 3 S31: -0.0804 S32: 0.0727 S33: -0.0709 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 170 THROUGH 224 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.6977 22.9483 -28.1417 REMARK 3 T TENSOR REMARK 3 T11: 0.0408 T22: 0.0501 REMARK 3 T33: 0.0667 T12: -0.0009 REMARK 3 T13: 0.0018 T23: 0.0165 REMARK 3 L TENSOR REMARK 3 L11: 0.7604 L22: 1.1621 REMARK 3 L33: 1.1134 L12: -0.1681 REMARK 3 L13: 0.0808 L23: 0.2568 REMARK 3 S TENSOR REMARK 3 S11: 0.0152 S12: 0.0355 S13: 0.0850 REMARK 3 S21: -0.0447 S22: 0.0053 S23: 0.0037 REMARK 3 S31: -0.0609 S32: 0.0010 S33: -0.0140 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 225 THROUGH 244 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.7813 27.0157 -35.2397 REMARK 3 T TENSOR REMARK 3 T11: 0.1067 T22: 0.0578 REMARK 3 T33: 0.1018 T12: 0.0069 REMARK 3 T13: -0.0023 T23: 0.0313 REMARK 3 L TENSOR REMARK 3 L11: 3.0773 L22: 1.0835 REMARK 3 L33: 2.6839 L12: 1.2671 REMARK 3 L13: -0.7232 L23: 0.1964 REMARK 3 S TENSOR REMARK 3 S11: -0.0549 S12: 0.1896 S13: 0.2366 REMARK 3 S21: -0.1779 S22: 0.0956 S23: 0.0727 REMARK 3 S31: -0.1767 S32: 0.0429 S33: 0.0213 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 245 THROUGH 341 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.2127 1.7861 -31.4819 REMARK 3 T TENSOR REMARK 3 T11: 0.0797 T22: 0.0792 REMARK 3 T33: 0.0684 T12: -0.0055 REMARK 3 T13: 0.0048 T23: 0.0052 REMARK 3 L TENSOR REMARK 3 L11: 0.2946 L22: 0.3032 REMARK 3 L33: 0.1724 L12: -0.1248 REMARK 3 L13: -0.0078 L23: 0.0343 REMARK 3 S TENSOR REMARK 3 S11: 0.0061 S12: 0.0390 S13: 0.0011 REMARK 3 S21: -0.0577 S22: -0.0045 S23: -0.0098 REMARK 3 S31: -0.0071 S32: 0.0157 S33: -0.0062 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 342 THROUGH 364 ) REMARK 3 ORIGIN FOR THE GROUP (A): 21.0905 -5.4090 -38.8307 REMARK 3 T TENSOR REMARK 3 T11: 0.1449 T22: 0.0886 REMARK 3 T33: 0.0845 T12: 0.0132 REMARK 3 T13: 0.0311 T23: 0.0034 REMARK 3 L TENSOR REMARK 3 L11: 1.5933 L22: 0.6087 REMARK 3 L33: 3.3767 L12: -0.7447 REMARK 3 L13: 0.4647 L23: -0.9007 REMARK 3 S TENSOR REMARK 3 S11: 0.0937 S12: 0.2079 S13: -0.0220 REMARK 3 S21: -0.2730 S22: -0.0888 S23: -0.1072 REMARK 3 S31: 0.2951 S32: 0.1043 S33: -0.0451 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 365 THROUGH 395 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.9534 7.7099 -29.8428 REMARK 3 T TENSOR REMARK 3 T11: 0.0779 T22: 0.0794 REMARK 3 T33: 0.0953 T12: -0.0186 REMARK 3 T13: 0.0117 T23: 0.0027 REMARK 3 L TENSOR REMARK 3 L11: 1.1798 L22: 0.8915 REMARK 3 L33: 1.3604 L12: -0.0140 REMARK 3 L13: 0.1487 L23: -0.2584 REMARK 3 S TENSOR REMARK 3 S11: -0.0377 S12: 0.1024 S13: 0.1093 REMARK 3 S21: -0.0835 S22: 0.0187 S23: -0.1491 REMARK 3 S31: -0.0609 S32: 0.0938 S33: -0.0493 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 7KDA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-OCT-20. REMARK 100 THE DEPOSITION ID IS D_1000252246. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-SEP-14 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 : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97915 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 105080 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.240 REMARK 200 RESOLUTION RANGE LOW (A) : 30.270 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.24 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.29 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : 0.27300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.800 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 (%): 42.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M LITHIUM CHLORIDE, 0.1 M 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 34.06200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 47.01400 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 58.44550 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 34.06200 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 47.01400 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 58.44550 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 34.06200 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 47.01400 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 58.44550 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 34.06200 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 47.01400 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 58.44550 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: 7870 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25030 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -44.0 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 655 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 749 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 943 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1058 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 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 HOH A 654 O HOH A 896 1.92 REMARK 500 O HOH A 761 O HOH A 801 1.94 REMARK 500 O HOH A 814 O HOH A 1025 1.99 REMARK 500 O HOH A 650 O HOH A 940 1.99 REMARK 500 O HOH A 981 O HOH A 1055 2.04 REMARK 500 O HOH A 932 O HOH A 940 2.07 REMARK 500 O HOH A 640 O HOH A 767 2.08 REMARK 500 O HOH A 819 O HOH A 915 2.08 REMARK 500 O HOH A 840 O HOH A 911 2.08 REMARK 500 O HOH A 923 O HOH A 929 2.10 REMARK 500 OE1 GLU A 347 O HOH A 601 2.14 REMARK 500 O HOH A 797 O HOH A 954 2.14 REMARK 500 O HOH A 1045 O HOH A 1065 2.16 REMARK 500 O HOH A 644 O HOH A 968 2.16 REMARK 500 O HOH A 738 O HOH A 927 2.16 REMARK 500 OH TYR A 235 O HOH A 602 2.17 REMARK 500 O HOH A 612 O HOH A 855 2.18 REMARK 500 O HOH A 678 O HOH A 954 2.18 REMARK 500 O HOH A 1077 O HOH A 1079 2.19 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 HD22 ASN A 105 HD22 ASN A 105 3555 1.32 REMARK 500 O HOH A 785 O HOH A 1018 7544 2.07 REMARK 500 O HOH A 718 O HOH A 936 8454 2.15 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. = 3.8 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 75.72 -118.73 REMARK 500 ASP A 191 84.99 -150.47 REMARK 500 VAL A 226 -68.31 -109.45 REMARK 500 THR A 270 -102.22 -120.07 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 A1076 DISTANCE = 5.95 ANGSTROMS REMARK 525 HOH A1077 DISTANCE = 6.51 ANGSTROMS REMARK 525 HOH A1078 DISTANCE = 7.29 ANGSTROMS REMARK 525 HOH A1079 DISTANCE = 7.46 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SAM A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TRS A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue WBM A 505 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7KCC RELATED DB: PDB REMARK 900 7KCC CONTAINS THE SAME PROTEIN COMPLEXED WITH COMPOUND AG-270 REMARK 900 RELATED ID: 7KCE RELATED DB: PDB REMARK 900 7KCE CONTAINS THE SAME PROTEIN COMPLEXED WITH COMPOUND 2 REMARK 900 RELATED ID: 7KCF RELATED DB: PDB REMARK 900 7KCF CONTAINS THE SAME PROTEIN COMPLEXED WITH COMPOUND 24512 REMARK 900 RELATED ID: 7KDB RELATED DB: PDB DBREF 7KDA A 1 395 UNP P31153 METK2_HUMAN 1 395 SEQADV 7KDA 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 501 46 HET CL A 502 1 HET TRS A 503 20 HET GOL A 504 9 HET WBM A 505 44 HETNAM SAM S-ADENOSYLMETHIONINE HETNAM CL CHLORIDE ION HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETNAM GOL GLYCEROL HETNAM WBM 2,3-DIPHENYL-5-[(1H-PYRAZOL-3-YL)AMINO]PYRAZOLO[1,5- HETNAM 2 WBM A]PYRIMIDIN-7(4H)-ONE HETSYN TRS TRIS BUFFER HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 SAM C15 H22 N6 O5 S FORMUL 3 CL CL 1- FORMUL 4 TRS C4 H12 N O3 1+ FORMUL 5 GOL C3 H8 O3 FORMUL 6 WBM C21 H16 N6 O FORMUL 7 HOH *479(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 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 22 HIS A 29 PRO A 30 ALA A 55 GLU A 70 SITE 2 AC1 22 GLN A 113 ASP A 116 ILE A 117 GLY A 133 SITE 3 AC1 22 ASP A 134 ASP A 179 LYS A 181 SER A 247 SITE 4 AC1 22 ARG A 249 PHE A 250 ASP A 258 LYS A 289 SITE 5 AC1 22 CL A 502 HOH A 715 HOH A 747 HOH A 757 SITE 6 AC1 22 HOH A 784 HOH A 813 SITE 1 AC2 5 HIS A 29 ASP A 134 LYS A 181 LYS A 265 SITE 2 AC2 5 SAM A 501 SITE 1 AC3 7 GLU A 85 ALA A 86 HIS A 89 GLN A 372 SITE 2 AC3 7 HOH A 645 HOH A 704 HOH A 708 SITE 1 AC4 12 ASP A 124 ARG A 125 ASN A 126 ALA A 229 SITE 2 AC4 12 VAL A 230 VAL A 231 PRO A 232 HOH A 632 SITE 3 AC4 12 HOH A 660 HOH A 686 HOH A 739 HOH A 877 SITE 1 AC5 13 PHE A 18 PHE A 20 GLN A 190 GLY A 273 SITE 2 AC5 13 TRP A 274 ARG A 313 LEU A 315 SER A 331 SITE 3 AC5 13 ILE A 332 PHE A 333 GLU A 342 HOH A 627 SITE 4 AC5 13 HOH A 822 CRYST1 68.124 94.028 116.891 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 0.014679 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010635 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008555 0.00000