HEADER ONCOPROTEIN 19-APR-22 7XKJ TITLE KRAS-G12D-GDP-MRTX1133 BY FIB-MICROED COMPND MOL_ID: 1; COMPND 2 MOLECULE: KRAS PROTO-ONCOGENE, GTPASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 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: MMYOMYO1_007468; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ONCOPROTEIN, G12D, GDP, GTPASE, HYDROLASE-HYDROLASE INHIBITOR KEYWDS 2 COMPLEX, HYDROLASE/HYDROLASE INHIBITOR, MICROED EXPDTA ELECTRON CRYSTALLOGRAPHY AUTHOR X.M.LI REVDAT 2 16-AUG-23 7XKJ 1 TITLE JRNL REVDAT 1 02-AUG-23 7XKJ 0 JRNL AUTH X.M.LI JRNL TITL KRAS-G12D-GDP-MRTX1133 BY FIB-MICROED JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.00 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) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.51 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 6411 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.313 REMARK 3 R VALUE (WORKING SET) : 0.310 REMARK 3 FREE R VALUE : 0.337 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.150 REMARK 3 FREE R VALUE TEST SET COUNT : 651 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 35.5100 - 5.1300 0.99 1154 130 0.3439 0.3314 REMARK 3 2 5.1200 - 4.0700 1.00 1159 132 0.2784 0.3093 REMARK 3 3 4.0700 - 3.5600 1.00 1144 133 0.2965 0.3657 REMARK 3 4 3.5600 - 3.2300 1.00 1164 131 0.3256 0.3269 REMARK 3 5 3.2300 - 3.0000 0.98 1139 125 0.3240 0.3757 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) : 0.384 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.245 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 44.23 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.68 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 1433 REMARK 3 ANGLE : 1.643 1952 REMARK 3 CHIRALITY : 0.092 213 REMARK 3 PLANARITY : 0.008 243 REMARK 3 DIHEDRAL : 17.300 529 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 7XKJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-APR-22. REMARK 100 THE DEPOSITION ID IS D_1300029004. REMARK 240 REMARK 240 EXPERIMENTAL DETAILS REMARK 240 RECONSTRUCTION METHOD : CRYSTALLOGRAPHY REMARK 240 SAMPLE TYPE : 3D ARRAY REMARK 240 SPECIMEN TYPE : NULL REMARK 240 DATA ACQUISITION REMARK 240 DATE OF DATA COLLECTION : NULL REMARK 240 TEMPERATURE (KELVIN) : NULL REMARK 240 PH : NULL REMARK 240 NUMBER OF CRYSTALS USED : NULL REMARK 240 MICROSCOPE MODEL : JEOL 2100F REMARK 240 DETECTOR TYPE : DIRECT ELECTRON DE-20 (5K X 3K) REMARK 240 ACCELERATION VOLTAGE (KV) : 200 REMARK 240 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 240 RESOLUTION RANGE HIGH (A) : NULL REMARK 240 RESOLUTION RANGE LOW (A) : NULL REMARK 240 DATA SCALING SOFTWARE : NULL REMARK 240 COMPLETENESS FOR RANGE (%) : NULL REMARK 240 DATA REDUNDANCY : NULL REMARK 240 IN THE HIGHEST RESOLUTION SHELL REMARK 240 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) :NULL REMARK 240 HIGHEST RESOLUTION SHELL, RANGE LOW (A) :NULL REMARK 240 COMPLETENESS FOR SHELL (%) : NULL REMARK 240 DATA REDUNDANCY IN SHELL : NULL REMARK 240 R MERGE FOR SHELL (I) : NULL REMARK 240 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 240 SOFTWARE USED : NULL REMARK 240 STARTING MODEL : NULL 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 19.44000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.60000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.64000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.60000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.44000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.64000 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: 250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 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 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 MET A 1 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 VAL A 44 CG1 CG2 REMARK 470 ASP A 57 CG OD1 OD2 REMARK 470 THR A 58 O REMARK 470 LEU A 79 CG CD1 CD2 REMARK 470 ILE A 93 CD1 REMARK 470 ARG A 97 CG CD NE CZ NH1 NH2 REMARK 470 ILE A 142 CG1 CG2 CD1 REMARK 470 ILE A 163 CD1 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 OG1 THR A 127 OE2 GLU A 143 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 OE1 GLN A 25 O TYR A 64 3544 1.59 REMARK 500 OE2 GLU A 168 N2 GDP A 201 1455 1.60 REMARK 500 OD2 ASP A 38 NE2 GLN A 99 3544 1.66 REMARK 500 OE1 GLU A 168 C2 GDP A 201 1455 2.02 REMARK 500 CD GLN A 25 O TYR A 64 3544 2.03 REMARK 500 OE1 GLU A 168 C4 GDP A 201 1455 2.10 REMARK 500 CD GLU A 168 N3 GDP A 201 1455 2.16 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 GLU A 31 76.46 -159.18 REMARK 500 LYS A 117 38.57 70.86 REMARK 500 ARG A 149 5.50 56.20 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 203 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 17 OG REMARK 620 2 GDP A 201 O3B 82.2 REMARK 620 N 1 DBREF1 7XKJ A 1 169 UNP A0A7J7Z4L6_MYOMY DBREF2 7XKJ A A0A7J7Z4L6 1 169 SEQADV 7XKJ ASP A 12 UNP A0A7J7Z4L GLY 12 ENGINEERED MUTATION SEQADV 7XKJ SER A 118 UNP A0A7J7Z4L 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 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 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 GDP A 201 28 HET 6IC A 202 44 HET MG A 203 1 HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM 6IC 4-(4-[(1R,5S)-3,8-DIAZABICYCLO[3.2.1]OCTAN-3-YL]-8- HETNAM 2 6IC FLUORO-2-{[(2R,4R,7AS)-2-FLUOROTETRAHYDRO-1H- HETNAM 3 6IC PYRROLIZIN-7A(5H)-YL]METHOXY}PYRIDO[4,3-D]PYRIMIDIN-7- HETNAM 4 6IC YL)-5-ETHYNYL-6-FLUORONAPHTHALEN-2-OL HETNAM MG MAGNESIUM ION HETSYN 6IC MRTX-1133 FORMUL 2 GDP C10 H15 N5 O11 P2 FORMUL 3 6IC C33 H31 F3 N6 O2 FORMUL 4 MG MG 2+ FORMUL 5 HOH *6(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 THR A 87 ASP A 105 1 19 HELIX 4 AA4 ASP A 126 TYR A 137 1 12 HELIX 5 AA5 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 CYS A 51 N VAL A 44 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 LEU A 79 N VAL A 7 SHEET 5 AA1 6 MET A 111 ASN A 116 1 O VAL A 114 N PHE A 82 SHEET 6 AA1 6 PHE A 141 GLU A 143 1 O ILE A 142 N GLY A 115 LINK OE1 GLU A 168 N3 GDP A 201 1555 1455 1.18 LINK OG SER A 17 MG MG A 203 1555 1555 2.12 LINK O3B GDP A 201 MG MG A 203 1555 1555 1.86 CRYST1 38.880 49.280 87.200 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 0.025720 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020292 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011468 0.00000