HEADER ONCOPROTEIN 30-AUG-23 8QDW TITLE NMR2 STRUCTURE OF KRAS G12V (GMPPNP BOUND) IN COMPLEX WITH N-METHYL-1- TITLE 2 (1-PHENYLPYRAZOL-4-YL)METHANAMINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RASK GTPASE (FRAGMENT); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: KRAS G12V GMPPNP BOUND SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: KRAS; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS COMPLEX, FRAGMENT, ONCOPROTEIN EXPDTA SOLUTION NMR NUMMDL 4 AUTHOR M.BUETIKOFER,J.ORTS REVDAT 1 11-SEP-24 8QDW 0 JRNL AUTH M.BUETIKOFER,J.ORTS JRNL TITL NMR2 STRUCTURE OF KRAS G12V (GMPPNP BOUND) IN COMPLEX WITH JRNL TITL 2 5-(1H-INDOL-2-L)PIPERAZIN-2-ONE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : HADDOCK REMARK 3 AUTHORS : BONVIN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8QDW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-AUG-23. REMARK 100 THE DEPOSITION ID IS D_1292133081. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.4 REMARK 210 IONIC STRENGTH : 130 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1 MM KRAS G12V GMPPNP, 5 MM N REMARK 210 -METHYL-1-(1-PHENYLPYRAZOL-4-YL)METHANAMINE, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-13C HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA, CCPNMR ANALYSIS REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 4 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 4 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-4 REMARK 465 RES C SSSEQI REMARK 465 LYS A 169 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 HZ2 LYS A 16 OD1 ASP A 57 1.57 REMARK 500 OD1 ASP A 132 HH21 ARG A 135 1.58 REMARK 500 OD2 ASP A 47 HH21 ARG A 161 1.59 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 1 ILE A 24 -71.52 -82.10 REMARK 500 1 GLU A 62 35.50 -91.89 REMARK 500 1 TYR A 64 58.12 -101.76 REMARK 500 1 PRO A 110 106.73 -56.06 REMARK 500 1 VAL A 152 -61.34 -103.19 REMARK 500 2 ALA A 11 -156.15 -110.50 REMARK 500 2 PRO A 34 97.83 -66.50 REMARK 500 2 GLU A 37 84.88 -159.69 REMARK 500 2 TYR A 64 57.80 -95.20 REMARK 500 2 ARG A 149 85.62 57.95 REMARK 500 3 ILE A 24 -71.59 -62.24 REMARK 500 3 ILE A 36 -79.27 -107.92 REMARK 500 3 TYR A 64 40.66 -100.52 REMARK 500 3 PRO A 110 97.79 -63.09 REMARK 500 3 ARG A 149 78.21 57.00 REMARK 500 4 PRO A 34 102.02 -59.63 REMARK 500 4 GLU A 37 87.33 -156.04 REMARK 500 4 GLU A 62 47.85 -104.83 REMARK 500 4 SER A 65 22.82 -142.82 REMARK 500 4 ARG A 149 70.28 56.34 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8QDK RELATED DB: PDB REMARK 900 RELATED ID: 34857 RELATED DB: BMRB REMARK 900 NMR2 STRUCTURE OF KRAS G12V (GMPPNP BOUND) IN COMPLEX WITH N-METHYL- REMARK 900 1-(1-PHENYLPYRAZOL-4-YL)METHANAMINE DBREF1 8QDW A 1 169 UNP A0A7L2RV33_9PASS DBREF2 8QDW A A0A7L2RV33 1 169 SEQADV 8QDW VAL A 12 UNP A0A7L2RV3 GLY 12 ENGINEERED MUTATION SEQADV 8QDW SER A 118 UNP A0A7L2RV3 CYS 118 CONFLICT SEQRES 1 A 169 MET THR GLU TYR LYS LEU VAL VAL VAL GLY ALA VAL 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 W1Y A 500 27 HETNAM W1Y N-METHYL-1-(1-PHENYL-1H-PYRAZOL-4-YL)METHANAMINE FORMUL 2 W1Y C11 H13 N3 HELIX 1 AA1 GLY A 15 GLN A 25 1 11 HELIX 2 AA2 GLN A 61 GLU A 63 5 3 HELIX 3 AA3 TYR A 64 GLY A 75 1 12 HELIX 4 AA4 ASN A 86 ASP A 105 1 20 HELIX 5 AA5 ASP A 126 GLY A 138 1 13 HELIX 6 AA6 VAL A 152 GLU A 168 1 17 SHEET 1 AA1 6 ASP A 38 ILE A 46 0 SHEET 2 AA1 6 GLU A 49 ASP A 57 -1 O GLU A 49 N ILE A 46 SHEET 3 AA1 6 GLU A 3 VAL A 9 1 N TYR A 4 O LEU A 52 SHEET 4 AA1 6 GLY A 77 ALA A 83 1 O GLY A 77 N VAL A 7 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 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1