HEADER HYDROLASE 28-MAY-25 9OUH TITLE K-RAS G12D CYSTEINE LIGHT AT 293 K COMPND MOL_ID: 1; COMPND 2 MOLECULE: ISOFORM 2B OF 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; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: 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 9OUH 0 JRNL AUTH M.XU,S.L.DECK,S.K.MILANO,R.A.CERIONE JRNL TITL ROOM TEMPERATURE STRUCTURES OF ONCOGENIC MUTANTS OF K-RAS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.40 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.33 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 29381 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.760 REMARK 3 FREE R VALUE TEST SET COUNT : 1987 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 41.3300 - 3.3800 1.00 2134 155 0.1802 0.2034 REMARK 3 2 3.3800 - 2.6800 1.00 2032 146 0.2004 0.2371 REMARK 3 3 2.6800 - 2.3400 1.00 1994 144 0.2086 0.2275 REMARK 3 4 2.3400 - 2.1300 1.00 1996 144 0.1949 0.2350 REMARK 3 5 2.1300 - 1.9800 1.00 1979 143 0.1988 0.2274 REMARK 3 6 1.9800 - 1.8600 1.00 1962 144 0.1993 0.2275 REMARK 3 7 1.8600 - 1.7700 1.00 1962 141 0.2127 0.2194 REMARK 3 8 1.7700 - 1.6900 0.99 1954 143 0.2127 0.2630 REMARK 3 9 1.6900 - 1.6300 0.99 1938 140 0.2079 0.2469 REMARK 3 10 1.6300 - 1.5700 0.99 1952 143 0.1936 0.2287 REMARK 3 11 1.5700 - 1.5200 0.98 1904 140 0.2027 0.1879 REMARK 3 12 1.5200 - 1.4800 0.97 1897 139 0.2160 0.2438 REMARK 3 13 1.4800 - 1.4400 0.96 1869 135 0.2219 0.2705 REMARK 3 14 1.4400 - 1.4000 0.93 1821 130 0.2425 0.2832 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) : 0.156 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.171 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.44 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 : 0.009 1413 REMARK 3 ANGLE : 1.190 1914 REMARK 3 CHIRALITY : 0.080 214 REMARK 3 PLANARITY : 0.008 245 REMARK 3 DIHEDRAL : 17.787 539 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 9OUH 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_1000296005. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-OCT-23 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : NULL 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) : 0.9686 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 : 36777 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 41.330 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 10.50 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 288.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.32 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 : 20.40 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 (%): 35.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG8000, 200 MM SODIUM ACETATE, REMARK 280 100 MM AMMONIUM ACETATE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 20.86700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.19100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.93550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.19100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.86700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.93550 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: 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: 8410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 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 33 112.56 -39.68 REMARK 500 GLU A 63 66.56 -68.46 REMARK 500 GLU A 108 78.39 -108.21 REMARK 500 ARG A 149 2.55 85.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 60 GLN A 61 -148.54 REMARK 500 REMARK 500 REMARK: NULL 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 202 O3B 91.7 REMARK 620 3 HOH A 330 O 171.9 89.6 REMARK 620 4 HOH A 340 O 94.2 87.6 93.9 REMARK 620 5 HOH A 371 O 92.6 171.1 87.3 84.3 REMARK 620 N 1 2 3 4 DBREF 9OUH A 1 169 UNP P01116 RASK_HUMAN 1 169 SEQADV 9OUH ASP A 12 UNP P01116 GLY 12 ENGINEERED MUTATION SEQADV 9OUH SER A 51 UNP P01116 CYS 51 ENGINEERED MUTATION SEQADV 9OUH LEU A 80 UNP P01116 CYS 80 ENGINEERED MUTATION SEQADV 9OUH GLU A 108 UNP P01116 ASP 108 CONFLICT SEQADV 9OUH SER A 118 UNP P01116 CYS 118 ENGINEERED MUTATION SEQRES 1 A 169 MET THR GLU TYR LYS LEU VAL VAL VAL GLY ALA ASP 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 SER 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 LEU 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 GLU VAL PRO MET VAL LEU VAL GLY ASN LYS SEQRES 10 A 169 SER 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 GDP A 202 28 HETNAM MG MAGNESIUM ION HETNAM GDP GUANOSINE-5'-DIPHOSPHATE FORMUL 2 MG MG 2+ FORMUL 3 GDP C10 H15 N5 O11 P2 FORMUL 4 HOH *163(H2 O) HELIX 1 AA1 GLY A 15 ASN A 26 1 12 HELIX 2 AA2 SER A 65 GLY A 75 1 11 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 LYS A 169 1 19 SHEET 1 AA1 6 ASP A 38 ILE A 46 0 SHEET 2 AA1 6 GLU A 49 ASP A 57 -1 O LEU A 53 N LYS A 42 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 2.08 LINK MG MG A 201 O3B GDP A 202 1555 1555 2.08 LINK MG MG A 201 O HOH A 330 1555 1555 2.12 LINK MG MG A 201 O HOH A 340 1555 1555 2.09 LINK MG MG A 201 O HOH A 371 1555 1555 2.08 CRYST1 41.734 51.871 68.382 90.00 90.00 90.00 P 21 21 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 0.023961 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019279 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014624 0.00000 CONECT 121 1363 CONECT 1363 121 1367 1421 1431 CONECT 1363 1462 CONECT 1364 1365 1366 1367 1368 CONECT 1365 1364 CONECT 1366 1364 CONECT 1367 1363 1364 CONECT 1368 1364 1369 CONECT 1369 1368 1370 1371 1372 CONECT 1370 1369 CONECT 1371 1369 CONECT 1372 1369 1373 CONECT 1373 1372 1374 CONECT 1374 1373 1375 1376 CONECT 1375 1374 1380 CONECT 1376 1374 1377 1378 CONECT 1377 1376 CONECT 1378 1376 1379 1380 CONECT 1379 1378 CONECT 1380 1375 1378 1381 CONECT 1381 1380 1382 1391 CONECT 1382 1381 1383 CONECT 1383 1382 1384 CONECT 1384 1383 1385 1391 CONECT 1385 1384 1386 1387 CONECT 1386 1385 CONECT 1387 1385 1388 CONECT 1388 1387 1389 1390 CONECT 1389 1388 CONECT 1390 1388 1391 CONECT 1391 1381 1384 1390 CONECT 1421 1363 CONECT 1431 1363 CONECT 1462 1363 MASTER 253 0 2 6 6 0 0 6 1550 1 34 13 END