HEADER SIGNALING PROTEIN/INHIBITOR 01-AUG-12 2LWI TITLE SOLUTION STRUCTURE OF H-RAST35S MUTANT PROTEIN IN COMPLEX WITH TITLE 2 KOBE2601 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 GTPASE HRAS, N-TERMINALLY PROCESSED; COMPND 7 ENGINEERED: YES; COMPND 8 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; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PGEX-6P-1 KEYWDS RAS, GTP-BOUND FORM, SIGNALING PROTEIN-INHIBITOR COMPLEX EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR M.ARAKI,A.TAMURA,F.SHIMA,T.KATAOKA REVDAT 2 24-AUG-22 2LWI 1 JRNL REMARK SEQADV LINK REVDAT 1 22-MAY-13 2LWI 0 JRNL AUTH F.SHIMA,Y.YOSHIKAWA,M.YE,M.ARAKI,S.MATSUMOTO,J.LIAO,L.HU, JRNL AUTH 2 T.SUGIMOTO,Y.IJIRI,A.TAKEDA,Y.NISHIYAMA,C.SATO,S.MURAOKA, JRNL AUTH 3 A.TAMURA,T.OSODA,K.TSUDA,T.MIYAKAWA,H.FUKUNISHI,J.SHIMADA, JRNL AUTH 4 T.KUMASAKA,M.YAMAMOTO,T.KATAOKA JRNL TITL IN SILICO DISCOVERY OF SMALL-MOLECULE RAS INHIBITORS THAT JRNL TITL 2 DISPLAY ANTITUMOR ACTIVITY BY BLOCKING THE RAS-EFFECTOR JRNL TITL 3 INTERACTION. JRNL REF PROC.NATL.ACAD.SCI.USA V. 110 8182 2013 JRNL REFN ESSN 1091-6490 JRNL PMID 23630290 JRNL DOI 10.1073/PNAS.1217730110 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 2.1, CNS 1.2 REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH (CYANA), REMARK 3 BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-KUNSTLEVE,JIANG,KUSZEWSKI, REMARK 3 NILGES, PANNU,READ,RICE,SIMONSON,WARREN (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANNEAL.INP REMARK 4 REMARK 4 2LWI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-AUG-12. REMARK 100 THE DEPOSITION ID IS D_1000102919. 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 : 0.22 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM [U-98% 13C; U-98% 15N] REMARK 210 ENTITY_1-1, 1 MM REMARK 210 PHOSPHOAMINOPHOSPHONIC ACID- REMARK 210 GUANYLATE ESTER-2, 8 MM REMARK 210 MAGNESIUM ION-3, 120 MM SODIUM REMARK 210 CHLORIDE-4, 20 MM SODIUM REMARK 210 PHOSPHATE-5, 3.8 MM KOB-6, 80% REMARK 210 D2O/20% DMSO_D6; 1 MM ENTITY_1-7, REMARK 210 1 MM PHOSPHOAMINOPHOSPHONIC REMARK 210 ACID-GUANYLATE ESTER-8, 8 MM REMARK 210 MAGNESIUM ION-9, 120 MM SODIUM REMARK 210 CHLORIDE-10, 20 MM SODIUM REMARK 210 PHOSPHATE-11, 3.8 MM KOB-12, 80% REMARK 210 D2O/20% DMSO_D6 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-13C HSQC; 3D 1H-13C NOESY; REMARK 210 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : DMX; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, SPARKY 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 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 1-15 REMARK 465 RES C SSSEQI REMARK 465 GLY A -5 REMARK 465 PRO A -4 REMARK 465 LEU A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 ASP A 0 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 -39.20 -179.46 REMARK 500 1 ILE A 24 -69.83 -90.81 REMARK 500 1 VAL A 29 105.36 -52.49 REMARK 500 1 PRO A 34 -167.33 -74.77 REMARK 500 1 GLU A 62 150.59 65.46 REMARK 500 1 TYR A 64 37.15 -176.17 REMARK 500 1 SER A 106 136.62 -172.27 REMARK 500 1 LYS A 117 67.70 61.96 REMARK 500 1 LEU A 120 165.38 -48.86 REMARK 500 1 ARG A 149 67.61 64.66 REMARK 500 2 ILE A 24 -72.08 -103.22 REMARK 500 2 PHE A 28 125.83 75.49 REMARK 500 2 ASP A 30 -37.28 177.29 REMARK 500 2 GLU A 63 91.30 46.68 REMARK 500 2 SER A 106 141.47 -173.27 REMARK 500 2 ALA A 121 35.04 -97.26 REMARK 500 2 ARG A 149 66.11 63.69 REMARK 500 3 ALA A 11 -36.13 176.79 REMARK 500 3 GLN A 25 -97.50 -94.56 REMARK 500 3 ASN A 26 70.11 163.11 REMARK 500 3 ASP A 30 -37.64 177.50 REMARK 500 3 GLU A 63 -79.38 -63.16 REMARK 500 3 LEU A 120 151.16 -49.81 REMARK 500 3 ARG A 149 65.52 62.88 REMARK 500 4 ILE A 24 -69.70 -99.42 REMARK 500 4 PHE A 28 127.90 74.70 REMARK 500 4 ASP A 30 -34.70 174.88 REMARK 500 4 GLU A 31 26.58 -142.80 REMARK 500 4 SER A 35 -175.94 -58.10 REMARK 500 4 ILE A 36 -170.73 46.58 REMARK 500 4 LEU A 53 76.93 -107.91 REMARK 500 4 GLU A 62 116.77 62.15 REMARK 500 4 GLU A 63 108.32 57.54 REMARK 500 4 TYR A 64 -86.97 -154.15 REMARK 500 4 LYS A 117 63.43 61.05 REMARK 500 4 ALA A 122 52.63 -143.20 REMARK 500 4 ARG A 149 63.68 63.13 REMARK 500 5 GLN A 25 -119.62 -84.14 REMARK 500 5 ASN A 26 39.06 179.69 REMARK 500 5 ASP A 30 -37.66 177.20 REMARK 500 5 GLU A 31 77.04 -116.44 REMARK 500 5 SER A 106 144.02 -178.74 REMARK 500 5 LYS A 117 74.06 60.77 REMARK 500 5 ARG A 149 72.26 63.64 REMARK 500 6 ALA A 11 -163.30 55.90 REMARK 500 6 ILE A 24 -70.84 -106.62 REMARK 500 6 ASN A 26 74.94 72.62 REMARK 500 6 ASP A 30 -44.55 -160.96 REMARK 500 6 SER A 35 88.66 55.34 REMARK 500 6 GLU A 37 -89.15 -101.28 REMARK 500 REMARK 500 THIS ENTRY HAS 150 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 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 17 OG REMARK 620 2 GNP A 201 O2G 166.8 REMARK 620 3 GNP A 201 O2B 90.9 79.3 REMARK 620 4 HOH A 301 O 81.2 90.9 95.6 REMARK 620 5 HOH A 302 O 92.4 96.4 90.3 171.4 REMARK 620 6 HOH A 303 O 92.4 95.9 170.3 75.9 98.6 REMARK 620 N 1 2 3 4 5 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 MG A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE KOB A 203 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 18629 RELATED DB: BMRB DBREF 2LWI A 1 166 UNP P01112 RASH_HUMAN 1 166 SEQADV 2LWI GLY A -5 UNP P01112 EXPRESSION TAG SEQADV 2LWI PRO A -4 UNP P01112 EXPRESSION TAG SEQADV 2LWI LEU A -3 UNP P01112 EXPRESSION TAG SEQADV 2LWI GLY A -2 UNP P01112 EXPRESSION TAG SEQADV 2LWI SER A -1 UNP P01112 EXPRESSION TAG SEQADV 2LWI ASP A 0 UNP P01112 EXPRESSION TAG SEQADV 2LWI SER A 35 UNP P01112 THR 35 ENGINEERED MUTATION SEQRES 1 A 172 GLY PRO LEU GLY SER ASP MET THR GLU TYR LYS LEU VAL SEQRES 2 A 172 VAL VAL GLY ALA GLY GLY VAL GLY LYS SER ALA LEU THR SEQRES 3 A 172 ILE GLN LEU ILE GLN ASN HIS PHE VAL ASP GLU TYR ASP SEQRES 4 A 172 PRO SER ILE GLU ASP SER TYR ARG LYS GLN VAL VAL ILE SEQRES 5 A 172 ASP GLY GLU THR CYS LEU LEU ASP ILE LEU ASP THR ALA SEQRES 6 A 172 GLY GLN GLU GLU TYR SER ALA MET ARG ASP GLN TYR MET SEQRES 7 A 172 ARG THR GLY GLU GLY PHE LEU CYS VAL PHE ALA ILE ASN SEQRES 8 A 172 ASN THR LYS SER PHE GLU ASP ILE HIS GLN TYR ARG GLU SEQRES 9 A 172 GLN ILE LYS ARG VAL LYS ASP SER ASP ASP VAL PRO MET SEQRES 10 A 172 VAL LEU VAL GLY ASN LYS CYS ASP LEU ALA ALA ARG THR SEQRES 11 A 172 VAL GLU SER ARG GLN ALA GLN ASP LEU ALA ARG SER TYR SEQRES 12 A 172 GLY ILE PRO TYR ILE GLU THR SER ALA LYS THR ARG GLN SEQRES 13 A 172 GLY VAL GLU ASP ALA PHE TYR THR LEU VAL ARG GLU ILE SEQRES 14 A 172 ARG GLN HIS HET GNP A 201 45 HET MG A 202 1 HET KOB A 203 34 HETNAM GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER HETNAM MG MAGNESIUM ION HETNAM KOB 2-(2,4-DINITROPHENYL)-N-(4-FLUOROPHENYL) HETNAM 2 KOB HYDRAZINECARBOTHIOAMIDE FORMUL 2 GNP C10 H17 N6 O13 P3 FORMUL 3 MG MG 2+ FORMUL 4 KOB C13 H10 F N5 O4 S FORMUL 5 HOH *3(H2 O) HELIX 1 1 GLY A 15 GLN A 25 1 11 HELIX 2 2 TYR A 64 GLY A 75 1 12 HELIX 3 3 ASN A 86 ASP A 105 1 20 HELIX 4 4 GLU A 126 GLY A 138 1 13 HELIX 5 5 GLY A 151 HIS A 166 1 16 SHEET 1 A 6 TYR A 40 ILE A 46 0 SHEET 2 A 6 GLU A 49 ASP A 57 -1 O ILE A 55 N TYR A 40 SHEET 3 A 6 GLU A 3 VAL A 9 1 N LEU A 6 O ASP A 54 SHEET 4 A 6 GLY A 77 ALA A 83 1 O LEU A 79 N VAL A 7 SHEET 5 A 6 MET A 111 ASN A 116 1 O VAL A 112 N CYS A 80 SHEET 6 A 6 TYR A 141 GLU A 143 1 O ILE A 142 N GLY A 115 LINK OG SER A 17 MG MG A 202 1555 1555 2.21 LINK O2G GNP A 201 MG MG A 202 1555 1555 2.08 LINK O2B GNP A 201 MG MG A 202 1555 1555 2.29 LINK MG MG A 202 O HOH A 301 1555 1555 2.30 LINK MG MG A 202 O HOH A 302 1555 1555 2.24 LINK MG MG A 202 O HOH A 303 1555 1555 2.24 SITE 1 AC1 12 GLY A 12 GLY A 13 GLY A 15 SER A 17 SITE 2 AC1 12 PHE A 28 ASN A 116 LYS A 117 LEU A 120 SITE 3 AC1 12 ALA A 146 LYS A 147 MG A 202 HOH A 301 SITE 1 AC2 5 SER A 17 GNP A 201 HOH A 301 HOH A 302 SITE 2 AC2 5 HOH A 303 SITE 1 AC3 6 LYS A 5 LEU A 56 ALA A 66 MET A 67 SITE 2 AC3 6 GLN A 70 TYR A 71 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