HEADER HYDROLASE 28-MAY-25 9OU2 TITLE K-RAS WILD TYPE 1-169 BOUND TO BI-2865 AT 100 K COMPND MOL_ID: 1; COMPND 2 MOLECULE: GTPASE KRAS; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: K-RAS 2,KI-RAS,C-K-RAS,C-KI-RAS; COMPND 5 EC: 3.6.5.2; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: KRAS, KRAS2, RASK2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS GTPASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.XU,S.L.DECK,S.K.MILANO,R.A.CERIONE REVDAT 1 17-JUN-26 9OU2 0 JRNL AUTH M.XU,S.L.DECK,S.K.MILANO,R.A.CERIONE JRNL TITL ONCOGENIC K-RAS MUTANTS BOUND TO INHIBITORS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.21.2_5419: ???) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.75 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 28579 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 46.7500 - 3.7300 0.96 2015 152 0.1828 0.1963 REMARK 3 2 3.7300 - 2.9600 0.94 1889 141 0.2132 0.2090 REMARK 3 3 2.9600 - 2.5800 0.96 1892 143 0.2343 0.2086 REMARK 3 4 2.5800 - 2.3500 0.98 1908 144 0.2189 0.2222 REMARK 3 5 2.3500 - 2.1800 0.99 1940 146 0.2261 0.2218 REMARK 3 6 2.1800 - 2.0500 0.99 1917 144 0.2291 0.2776 REMARK 3 7 2.0500 - 1.9500 0.99 1919 144 0.2471 0.2468 REMARK 3 8 1.9500 - 1.8600 0.99 1908 144 0.2372 0.2329 REMARK 3 9 1.8600 - 1.7900 0.98 1896 142 0.2223 0.2288 REMARK 3 10 1.7900 - 1.7300 0.98 1887 143 0.2249 0.2310 REMARK 3 11 1.7300 - 1.6800 0.99 1873 140 0.2388 0.2224 REMARK 3 12 1.6800 - 1.6300 0.98 1887 143 0.2485 0.2617 REMARK 3 13 1.6300 - 1.5900 0.97 1860 140 0.2606 0.2486 REMARK 3 14 1.5900 - 1.5500 0.93 1788 134 0.2913 0.2881 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.360 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.75 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.012 1447 REMARK 3 ANGLE : 1.403 1964 REMARK 3 CHIRALITY : 0.065 217 REMARK 3 PLANARITY : 0.010 247 REMARK 3 DIHEDRAL : 17.338 548 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 9OU2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-MAY-25. REMARK 100 THE DEPOSITION ID IS D_1000293269. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-APR-25 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : 7B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29414 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 46.750 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 200 DATA REDUNDANCY : 1.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 77.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.57 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 : 4.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG2000, 0.2 MM MAGNESIUM REMARK 280 CHLORIDE, 100 MM SODIUM ACETATE, PH 4.6, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 2 21 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+1/2,-Y,-Z+1/2 REMARK 290 4555 -X+1/2,-Y,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 20.23700 REMARK 290 SMTRY2 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.50100 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 20.23700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 43.50100 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 870 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 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 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 ASP A 33 114.88 -35.78 REMARK 500 TYR A 64 62.00 -111.80 REMARK 500 LYS A 117 37.89 71.85 REMARK 500 SER A 122 50.13 -92.36 REMARK 500 ASP A 126 153.36 -46.45 REMARK 500 ARG A 149 -4.44 83.94 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 424 DISTANCE = 5.81 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 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 17 OG REMARK 620 2 GDP A 203 O2B 94.3 REMARK 620 3 HOH A 323 O 80.3 98.3 REMARK 620 4 HOH A 342 O 171.2 90.6 91.7 REMARK 620 5 HOH A 351 O 92.8 90.3 169.2 94.5 REMARK 620 6 HOH A 369 O 92.6 171.3 88.1 83.3 84.0 REMARK 620 N 1 2 3 4 5 DBREF 9OU2 A 1 169 UNP P01116 RASK_HUMAN 1 169 SEQRES 1 A 169 MET THR GLU TYR LYS LEU VAL VAL VAL GLY ALA GLY GLY SEQRES 2 A 169 VAL GLY LYS SER ALA LEU THR ILE GLN LEU ILE GLN ASN SEQRES 3 A 169 HIS PHE VAL ASP GLU TYR ASP PRO THR ILE GLU ASP SER SEQRES 4 A 169 TYR ARG LYS GLN VAL VAL ILE ASP GLY GLU THR CYS LEU SEQRES 5 A 169 LEU ASP ILE LEU ASP THR ALA GLY GLN GLU GLU TYR SER SEQRES 6 A 169 ALA MET ARG ASP GLN TYR MET ARG THR GLY GLU GLY PHE SEQRES 7 A 169 LEU CYS VAL PHE ALA ILE ASN ASN THR LYS SER PHE GLU SEQRES 8 A 169 ASP ILE HIS HIS TYR ARG GLU GLN ILE LYS ARG VAL LYS SEQRES 9 A 169 ASP SER GLU ASP VAL PRO MET VAL LEU VAL GLY ASN LYS SEQRES 10 A 169 CYS ASP LEU PRO SER ARG THR VAL ASP THR LYS GLN ALA SEQRES 11 A 169 GLN ASP LEU ALA ARG SER TYR GLY ILE PRO PHE ILE GLU SEQRES 12 A 169 THR SER ALA LYS THR ARG GLN GLY VAL ASP ASP ALA PHE SEQRES 13 A 169 TYR THR LEU VAL ARG GLU ILE ARG LYS HIS LYS GLU LYS HET MG A 201 1 HET OFU A 202 33 HET GDP A 203 28 HETNAM MG MAGNESIUM ION HETNAM OFU (4S)-2-AZANYL-4-METHYL-4-[3-[4-[(1S)-1-[(2S)-1- HETNAM 2 OFU METHYLPYRROLIDIN-1-IUM-2-YL]ETHOXY]PYRIMIDIN-2-YL]-1, HETNAM 3 OFU 2,4-OXADIAZOL-5-YL]-6,7-DIHYDRO-5H-1-BENZOTHIOPHENE-3- HETNAM 4 OFU CARBONITRILE HETNAM GDP GUANOSINE-5'-DIPHOSPHATE FORMUL 2 MG MG 2+ FORMUL 3 OFU C23 H28 N7 O2 S 1+ FORMUL 4 GDP C10 H15 N5 O11 P2 FORMUL 5 HOH *124(H2 O) HELIX 1 AA1 GLY A 15 ASN A 26 1 12 HELIX 2 AA2 SER A 65 THR A 74 1 10 HELIX 3 AA3 ASN A 86 ASP A 92 1 7 HELIX 4 AA4 ASP A 92 ASP A 105 1 14 HELIX 5 AA5 ASP A 126 GLY A 138 1 13 HELIX 6 AA6 GLY A 151 GLU A 168 1 18 SHEET 1 AA1 6 ASP A 38 ILE A 46 0 SHEET 2 AA1 6 GLU A 49 ASP A 57 -1 O ILE A 55 N TYR A 40 SHEET 3 AA1 6 GLU A 3 VAL A 9 1 N VAL A 8 O LEU A 56 SHEET 4 AA1 6 GLY A 77 ALA A 83 1 O VAL A 81 N VAL A 9 SHEET 5 AA1 6 MET A 111 ASN A 116 1 O ASN A 116 N PHE A 82 SHEET 6 AA1 6 PHE A 141 GLU A 143 1 O ILE A 142 N LEU A 113 LINK OG SER A 17 MG MG A 201 1555 1555 2.05 LINK MG MG A 201 O2B GDP A 203 1555 1555 1.87 LINK MG MG A 201 O HOH A 323 1555 1555 1.97 LINK MG MG A 201 O HOH A 342 1555 1555 2.07 LINK MG MG A 201 O HOH A 351 1555 1555 1.97 LINK MG MG A 201 O HOH A 369 1555 1555 2.11 CRYST1 40.474 55.440 87.002 90.00 90.00 90.00 P 21 2 21 4 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 0.024707 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018038 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011494 0.00000 CONECT 117 1360 CONECT 1360 117 1396 1444 1463 CONECT 1360 1472 1490 CONECT 1361 1362 1381 CONECT 1362 1361 1363 CONECT 1363 1362 1386 CONECT 1364 1381 1383 1392 CONECT 1365 1366 1375 CONECT 1366 1365 1376 1392 CONECT 1367 1377 1379 CONECT 1368 1377 1378 CONECT 1369 1370 1378 1379 CONECT 1370 1369 1371 1382 CONECT 1371 1370 1389 1393 CONECT 1372 1378 CONECT 1373 1375 1387 1388 CONECT 1374 1386 CONECT 1375 1365 1373 1385 CONECT 1376 1366 1384 CONECT 1377 1367 1368 CONECT 1378 1368 1369 1372 1380 CONECT 1379 1367 1369 1393 CONECT 1380 1378 1388 1391 CONECT 1381 1361 1364 1386 CONECT 1382 1370 1390 CONECT 1383 1364 CONECT 1384 1376 1385 CONECT 1385 1375 1384 CONECT 1386 1363 1374 1381 CONECT 1387 1373 1391 CONECT 1388 1373 1380 CONECT 1389 1371 CONECT 1390 1382 CONECT 1391 1380 1387 CONECT 1392 1364 1366 CONECT 1393 1371 1379 CONECT 1394 1395 1396 1397 1398 CONECT 1395 1394 CONECT 1396 1360 1394 CONECT 1397 1394 CONECT 1398 1394 1399 CONECT 1399 1398 1400 1401 1402 CONECT 1400 1399 CONECT 1401 1399 CONECT 1402 1399 1403 CONECT 1403 1402 1404 CONECT 1404 1403 1405 1406 CONECT 1405 1404 1410 CONECT 1406 1404 1407 1408 CONECT 1407 1406 CONECT 1408 1406 1409 1410 CONECT 1409 1408 CONECT 1410 1405 1408 1411 CONECT 1411 1410 1412 1421 CONECT 1412 1411 1413 CONECT 1413 1412 1414 CONECT 1414 1413 1415 1421 CONECT 1415 1414 1416 1417 CONECT 1416 1415 CONECT 1417 1415 1418 CONECT 1418 1417 1419 1420 CONECT 1419 1418 CONECT 1420 1418 1421 CONECT 1421 1411 1414 1420 CONECT 1444 1360 CONECT 1463 1360 CONECT 1472 1360 CONECT 1490 1360 MASTER 257 0 3 6 6 0 0 6 1536 1 68 13 END