HEADER ONCOPROTEIN 15-FEB-18 5ZC6 TITLE SOLUTION STRUCTURE OF H-RAST35S MUTANT PROTEIN IN COMPLEX WITH KBFM123 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GTPASE HRAS; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1-166; COMPND 5 SYNONYM: H-RAS-1,HA-RAS,TRANSFORMING PROTEIN P21,C-H-RAS,P21RAS; 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: HRAS, HRAS1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS INHIBITOR, COMPLEX, CANCER, SMALL GTPASES, ONCOPROTEIN EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR S.MATSUMOTO,Y.HAYASHI,T.HIRAGA,K.MATSUO,T.KATAOKA REVDAT 3 01-MAY-24 5ZC6 1 REMARK REVDAT 2 26-SEP-18 5ZC6 1 JRNL REVDAT 1 12-SEP-18 5ZC6 0 JRNL AUTH S.MATSUMOTO,T.HIRAGA,Y.HAYASHI,Y.YOSHIKAWA,C.TSUDA,M.ARAKI, JRNL AUTH 2 M.NEYA,F.SHIMA,T.KATAOKA JRNL TITL MOLECULAR BASIS FOR ALLOSTERIC INHIBITION OF GTP-BOUND H-RAS JRNL TITL 2 PROTEIN BY A SMALL-MOLECULE COMPOUND CARRYING A NAPHTHALENE JRNL TITL 3 RING JRNL REF BIOCHEMISTRY V. 57 5350 2018 JRNL REFN ISSN 1520-4995 JRNL PMID 30141910 JRNL DOI 10.1021/ACS.BIOCHEM.8B00680 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER A. T. ET.AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5ZC6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-FEB-18. REMARK 100 THE DEPOSITION ID IS D_1300006648. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 50 REMARK 210 PRESSURE : AMBIENT PA REMARK 210 SAMPLE CONTENTS : 0.8 MM [U-99% 13C; U-99% 15N] H REMARK 210 -RAST35S, 3.0 MM KBFM123, 20 MM REMARK 210 SODIUM PHOSPHATE, 40 MM SODIUM REMARK 210 CHLORIDE, 8 MM MAGNESIUM ION, REMARK 210 0.8 MM PHOSPHOAMINOPHOSPHONIC REMARK 210 ACID-GUANYLATE ESTER, 80% D2O/20% REMARK 210 D6-DMSO REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 3D 1H-13C NOESY; REMARK 210 2D 1H-13C HSQC ALIPHATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 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 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 ALA A 11 -77.49 -59.70 REMARK 500 1 VAL A 29 -163.65 -60.33 REMARK 500 1 ASP A 30 32.69 75.07 REMARK 500 1 GLU A 31 32.34 -172.20 REMARK 500 1 ASP A 38 -29.27 89.03 REMARK 500 1 GLN A 61 46.77 -108.47 REMARK 500 1 GLU A 62 11.74 -141.58 REMARK 500 1 GLU A 63 29.45 46.65 REMARK 500 1 SER A 65 -54.41 -128.65 REMARK 500 1 GLU A 76 -67.92 -93.67 REMARK 500 1 ASP A 107 -51.28 -126.00 REMARK 500 1 LEU A 120 -85.52 -65.39 REMARK 500 1 ALA A 121 -46.53 165.16 REMARK 500 2 ALA A 11 -167.24 -68.32 REMARK 500 2 VAL A 14 28.05 44.02 REMARK 500 2 VAL A 29 -161.67 -62.90 REMARK 500 2 ASP A 30 -48.77 86.99 REMARK 500 2 SER A 35 -62.49 79.79 REMARK 500 2 ASP A 38 -68.26 67.04 REMARK 500 2 GLN A 61 -151.99 -106.03 REMARK 500 2 GLU A 62 -172.82 78.20 REMARK 500 2 GLU A 63 30.41 -97.96 REMARK 500 2 SER A 65 -43.24 -178.09 REMARK 500 2 GLU A 76 -68.97 -97.23 REMARK 500 2 SER A 106 -94.18 -139.77 REMARK 500 2 ASP A 107 -66.28 158.80 REMARK 500 2 LEU A 120 -178.04 -56.66 REMARK 500 3 VAL A 29 -159.47 -59.46 REMARK 500 3 ASP A 30 -0.74 82.44 REMARK 500 3 ASP A 38 -23.08 84.30 REMARK 500 3 GLU A 63 100.80 61.01 REMARK 500 3 ASP A 105 47.58 37.68 REMARK 500 3 ASP A 107 -58.31 75.35 REMARK 500 3 LEU A 120 -84.03 -68.68 REMARK 500 3 ALA A 121 -39.71 168.99 REMARK 500 4 VAL A 29 -166.28 -56.59 REMARK 500 4 ASP A 30 -42.52 87.97 REMARK 500 4 ASP A 38 -2.50 80.64 REMARK 500 4 GLU A 63 94.00 70.15 REMARK 500 4 SER A 65 -57.35 -142.89 REMARK 500 4 LEU A 120 -172.08 -55.84 REMARK 500 4 ALA A 122 64.83 -158.52 REMARK 500 5 ALA A 11 -171.19 171.01 REMARK 500 5 VAL A 14 -47.44 -139.74 REMARK 500 5 VAL A 29 159.46 -48.35 REMARK 500 5 ASP A 30 44.50 113.41 REMARK 500 5 GLU A 31 -42.47 -171.14 REMARK 500 5 SER A 35 -2.16 78.22 REMARK 500 5 GLU A 62 148.85 -176.85 REMARK 500 5 GLU A 63 78.10 -65.04 REMARK 500 REMARK 500 THIS ENTRY HAS 177 RAMACHANDRAN OUTLIERS. 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 GNP A 201 O1G 177.3 REMARK 620 3 GNP A 201 O2B 90.6 88.2 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GNP A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue KBF A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 203 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 18629 RELATED DB: BMRB REMARK 900 RELATED ID: 2LWI RELATED DB: PDB REMARK 900 RELATED ID: 17610 RELATED DB: BMRB REMARK 900 RELATED ID: 2LCF RELATED DB: PDB REMARK 900 RELATED ID: 36166 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF H-RAST35S MUTANT PROTEIN IN COMPLEX WITH REMARK 900 KBFM123 DBREF 5ZC6 A 1 166 UNP P01112 RASH_HUMAN 1 166 SEQADV 5ZC6 SER A 35 UNP P01112 THR 35 ENGINEERED MUTATION SEQRES 1 A 166 MET THR GLU TYR LYS LEU VAL VAL VAL GLY ALA GLY GLY SEQRES 2 A 166 VAL GLY LYS SER ALA LEU THR ILE GLN LEU ILE GLN ASN SEQRES 3 A 166 HIS PHE VAL ASP GLU TYR ASP PRO SER ILE GLU ASP SER SEQRES 4 A 166 TYR ARG LYS GLN VAL VAL ILE ASP GLY GLU THR CYS LEU SEQRES 5 A 166 LEU ASP ILE LEU ASP THR ALA GLY GLN GLU GLU TYR SER SEQRES 6 A 166 ALA MET ARG ASP GLN TYR MET ARG THR GLY GLU GLY PHE SEQRES 7 A 166 LEU CYS VAL PHE ALA ILE ASN ASN THR LYS SER PHE GLU SEQRES 8 A 166 ASP ILE HIS GLN TYR ARG GLU GLN ILE LYS ARG VAL LYS SEQRES 9 A 166 ASP SER ASP ASP VAL PRO MET VAL LEU VAL GLY ASN LYS SEQRES 10 A 166 CYS ASP LEU ALA ALA ARG THR VAL GLU SER ARG GLN ALA SEQRES 11 A 166 GLN ASP LEU ALA ARG SER TYR GLY ILE PRO TYR ILE GLU SEQRES 12 A 166 THR SER ALA LYS THR ARG GLN GLY VAL GLU ASP ALA PHE SEQRES 13 A 166 TYR THR LEU VAL ARG GLU ILE ARG GLN HIS HET GNP A 201 45 HET KBF A 202 37 HET MG A 203 1 HETNAM GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER HETNAM KBF 3-OXIDANYL-~{N}-[[(2~{R})-OXOLAN-2- HETNAM 2 KBF YL]METHYL]NAPHTHALENE-2-CARBOXAMIDE HETNAM MG MAGNESIUM ION HETSYN KBF 3-HYDROXY-N-(TETRAHYDROFURAN-2-YLMETHYL)NAPHTHALENE-2- HETSYN 2 KBF CARBOXAMIDE FORMUL 2 GNP C10 H17 N6 O13 P3 FORMUL 3 KBF C16 H17 N O3 FORMUL 4 MG MG 2+ HELIX 1 AA1 GLY A 15 GLN A 25 1 11 HELIX 2 AA2 SER A 65 GLY A 75 1 11 HELIX 3 AA3 ASN A 86 ASP A 105 1 20 HELIX 4 AA4 GLU A 126 SER A 136 1 11 HELIX 5 AA5 GLY A 151 HIS A 166 1 16 SHEET 1 AA1 6 GLN A 43 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 LEU A 6 O LEU A 56 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 VAL A 114 N CYS A 80 SHEET 6 AA1 6 TYR A 141 GLU A 143 1 O ILE A 142 N LEU A 113 LINK OG SER A 17 MG MG A 203 1555 1555 2.23 LINK O1G GNP A 201 MG MG A 203 1555 1555 2.04 LINK O2B GNP A 201 MG MG A 203 1555 1555 2.15 SITE 1 AC1 13 GLY A 12 VAL A 14 LYS A 16 SER A 17 SITE 2 AC1 13 PHE A 28 VAL A 29 ASP A 30 ASN A 116 SITE 3 AC1 13 LYS A 117 LEU A 120 ALA A 146 LYS A 147 SITE 4 AC1 13 MG A 203 SITE 1 AC2 5 LYS A 5 ASP A 38 LEU A 56 TYR A 71 SITE 2 AC2 5 THR A 74 SITE 1 AC3 2 SER A 17 GNP A 201 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