HEADER HYDROLASE 20-JAN-21 7LGI TITLE THE HADDOCK MODEL OF GDP KRAS IN COMPLEX WITH PROMAZINE USING CHEMICAL TITLE 2 SHIFT PERTURBATIONS AND INTERMOLECULAR NOES 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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GDP KRAS, SMALL MOLECULE LIGAND, HADDOCK STRUCTURE MODEL, CHEMICAL KEYWDS 2 SHIFT CHANGES, INTERMOLECULAR NOE, HYDROLASE EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR X.WANG,A.A.GORFE,J.A.PUTKEY REVDAT 2 01-MAY-24 7LGI 1 REMARK REVDAT 1 21-JUL-21 7LGI 0 JRNL AUTH X.WANG,A.A.GORFE,J.A.PUTKEY JRNL TITL ANTIPSYCHOTIC PHENOTHIAZINE DRUGS BIND TO KRAS IN VITRO. JRNL REF J.BIOMOL.NMR V. 75 233 2021 JRNL REFN ISSN 0925-2738 JRNL PMID 34176062 JRNL DOI 10.1007/S10858-021-00371-Z REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : HADDOCK REMARK 3 AUTHORS : A.M.J.J. BONVIN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7LGI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-JAN-21. REMARK 100 THE DEPOSITION ID IS D_1000254260. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 298 REMARK 210 PH : 7.4; 7.4 REMARK 210 IONIC STRENGTH : 115; 115 REMARK 210 PRESSURE : 1 PA ATM; 1 PA ATM REMARK 210 SAMPLE CONTENTS : 0.8 MM [U-99% 13C; U-99% 15N] REMARK 210 KRAS, 1.0 MM P2Z, 5 MM [U-99% 2H] REMARK 210 DTT, 10 UM [U-99% 2H] DSS, 25 REMARK 210 MM SODIUM PHOSPHATE, 50 MM REMARK 210 SODIUM CHLORIDE, 90% H2O/10% D2O; REMARK 210 0.8 MM [U-99% 13C; U-99% 15N] REMARK 210 KRAS, 1.0 MM P2Z, 5 MM [U-99% 2H] REMARK 210 DTT, 10 UM [U-99% 2H] DSS, 25 REMARK 210 MM SODIUM PHOSPHATE, 50 MM REMARK 210 SODIUM CHLORIDE, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D CBCA(CO)NH; REMARK 210 3D HNCACB; 3D C(CO)NH; 3D H(CCO) REMARK 210 NH; 2D 1H-13C HSQC; 3D CCH-TOCSY; REMARK 210 3D 1H-13C NOESY ALIPHATIC; 15N- REMARK 210 FILTERED 3D NOESY- 1H; 2D 1H-13C REMARK 210 HSQC ALIPHATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 1.3, NMRPIPE 2.2, REMARK 210 NMRVIEWJ REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1000 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 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 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: 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 OD2 ASP A 57 MG MG A 202 1.55 REMARK 500 HZ3 LYS A 101 OE1 GLU A 107 1.56 REMARK 500 HZ2 LYS A 5 OD2 ASP A 54 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 PRO A 110 104.96 -54.74 REMARK 500 1 LYS A 117 33.59 71.23 REMARK 500 2 ALA A 18 -58.97 -130.80 REMARK 500 2 SER A 122 68.92 61.73 REMARK 500 3 VAL A 14 -84.74 -81.01 REMARK 500 3 PRO A 110 106.09 -54.87 REMARK 500 3 ARG A 149 87.61 63.79 REMARK 500 4 ILE A 24 -61.64 -90.60 REMARK 500 4 LYS A 117 36.01 74.78 REMARK 500 7 ASP A 57 66.73 -106.94 REMARK 500 7 PRO A 110 108.84 -58.54 REMARK 500 7 ARG A 149 -3.11 73.68 REMARK 500 8 ASP A 57 69.20 -116.51 REMARK 500 8 PRO A 110 102.98 -58.69 REMARK 500 9 ALA A 59 -80.21 -85.85 REMARK 500 10 PRO A 110 109.18 -56.82 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 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 17 OG REMARK 620 2 ASP A 57 OD1 69.0 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GDP A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue P2Z A 203 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30694 RELATED DB: BMRB REMARK 900 THE HADDOCK MODEL OF GDP KRAS IN COMPLEX WITH A SMALL MOLECULE REMARK 900 LIGAND REMARK 900 RELATED ID: 6V5L RELATED DB: PDB REMARK 900 THE HADDOCK MODEL OF GDP KRAS IN COMPLEX WITH A SMALL MOLECULE REMARK 900 LIGAND REMARK 900 RELATED ID: 30845 RELATED DB: BMRB REMARK 900 THE HADDOCK MODEL OF GDP KRAS IN COMPLEX WITH A SMALL MOLECULE REMARK 900 LIGAND DBREF 7LGI 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 GDP A 201 40 HET MG A 202 1 HET P2Z A 203 40 HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM P2Z PROMAZINE HETSYN P2Z N,N-DIMETHYL-3-(10H-PHENOTHIAZIN-10-YL)PROPAN-1-AMINE FORMUL 2 GDP C10 H15 N5 O11 P2 FORMUL 3 MG MG 2+ FORMUL 4 P2Z C17 H20 N2 S HELIX 1 AA1 GLY A 15 GLN A 25 1 11 HELIX 2 AA2 TYR A 64 TYR A 71 1 8 HELIX 3 AA3 ASN A 86 ASP A 105 1 20 HELIX 4 AA4 ASP A 126 GLY A 138 1 13 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 THR A 2 GLY A 10 1 N TYR A 4 O ASP A 54 SHEET 4 AA1 6 GLY A 77 ALA A 83 1 O LEU A 79 N VAL A 9 SHEET 5 AA1 6 MET A 111 ASN A 116 1 O VAL A 114 N CYS A 80 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 202 1555 1555 1.72 LINK OD1 ASP A 57 MG MG A 202 1555 1555 2.72 SITE 1 AC1 16 GLY A 13 VAL A 14 GLY A 15 LYS A 16 SITE 2 AC1 16 SER A 17 ALA A 18 PHE A 28 VAL A 29 SITE 3 AC1 16 ASP A 30 TYR A 32 PRO A 34 ASP A 57 SITE 4 AC1 16 ASN A 116 LEU A 120 ALA A 146 LYS A 147 SITE 1 AC2 3 SER A 17 ILE A 36 ASP A 57 SITE 1 AC3 8 LYS A 5 VAL A 7 GLU A 37 ARG A 41 SITE 2 AC3 8 ASP A 54 LEU A 56 TYR A 71 THR A 74 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 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