PDB Short entry for 1AA9 HEADER PROTO-ONCOGENE 27-JAN-97 1AA9 TITLE HUMAN C-HA-RAS(1-171)(DOT)GDP, NMR, MINIMIZED AVERAGE STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: C-HA-RAS; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1 - 171; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: COMPLEXED TO GUANOSINE 5'-DIPHOSPHATE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: HUMAN C-HA-RAS GENE; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: TG1; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PRGH; SOURCE 10 EXPRESSION_SYSTEM_GENE: HUMAN C-HA-RAS GENE KEYWDS RAS, ONCOGENE PROTEIN, GTP-BINDING PROTEIN, PROTO-ONCOGENE, RIKEN KEYWDS 2 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, STRUCTURAL GENOMICS EXPDTA SOLUTION NMR AUTHOR Y.ITO,Y.YAMASAKI,Y.MUTO,G.KAWAI,S.NISHIMURA,T.MIYAZAWA,S.YOKOYAMA, AUTHOR 2 RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 3 16-FEB-22 1AA9 1 REMARK LINK REVDAT 2 24-FEB-09 1AA9 1 VERSN REVDAT 1 29-JUL-97 1AA9 0 JRNL AUTH Y.ITO,K.YAMASAKI,J.IWAHARA,T.TERADA,A.KAMIYA,M.SHIROUZU, JRNL AUTH 2 Y.MUTO,G.KAWAI,S.YOKOYAMA,E.D.LAUE,M.WALCHLI,T.SHIBATA, JRNL AUTH 3 S.NISHIMURA,T.MIYAZAWA JRNL TITL REGIONAL POLYSTERISM IN THE GTP-BOUND FORM OF THE HUMAN JRNL TITL 2 C-HA-RAS PROTEIN. JRNL REF BIOCHEMISTRY V. 36 9109 1997 JRNL REFN ISSN 0006-2960 JRNL PMID 9230043 JRNL DOI 10.1021/BI970296U REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: SIMULATED ANNEALING REFINEMENT FOR NMR REMARK 3 STRUCTURE DETERMINATION. REMARK 4 REMARK 4 1AA9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000170587. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 5.5 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 1H-1H NOESY; 1H-15N HSQC; 1H-13C REMARK 210 HSQC; HMQC-J; 3D 15N-SEPARATED REMARK 210 NOESY; 3D 13C-SEPARATED NOESY; REMARK 210 HNHB; HN(CO)HB; HNCA; HN(CO)CA; REMARK 210 HNCO; HNCACB; HCACO; HCCH-COSY; REMARK 210 HCCH-TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 400 MHZ REMARK 210 SPECTROMETER MODEL : AMX600; ARX400 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 2.3, AZARA 1.0, X-PLOR 3.1 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 30 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : MINIMIZED AVERAGE STRUCTURE REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL 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 O ILE A 46 N GLY A 48 2.19 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 LYS A 5 93.13 -48.69 REMARK 500 ALA A 18 -42.38 -29.39 REMARK 500 ILE A 24 -80.32 -104.09 REMARK 500 PRO A 34 42.38 -79.70 REMARK 500 THR A 35 -38.18 -147.92 REMARK 500 ILE A 36 177.86 -49.13 REMARK 500 GLU A 37 123.37 -171.05 REMARK 500 LYS A 42 136.47 176.89 REMARK 500 VAL A 44 -163.31 -128.00 REMARK 500 ASP A 47 74.71 -30.03 REMARK 500 GLU A 49 -133.18 -110.74 REMARK 500 THR A 58 137.28 67.38 REMARK 500 ALA A 59 -165.59 -109.97 REMARK 500 GLN A 61 24.74 44.06 REMARK 500 GLU A 62 -97.72 -143.12 REMARK 500 GLU A 63 -57.69 -163.92 REMARK 500 TYR A 64 -106.52 -146.45 REMARK 500 ARG A 68 56.19 -90.06 REMARK 500 LYS A 88 -75.56 -39.57 REMARK 500 TYR A 96 -72.17 -63.48 REMARK 500 ILE A 100 -74.55 -54.16 REMARK 500 LYS A 101 -28.15 -37.44 REMARK 500 LYS A 104 -91.82 -53.34 REMARK 500 ASP A 105 -51.88 -162.37 REMARK 500 SER A 106 -163.88 -128.60 REMARK 500 ASP A 108 45.30 -145.27 REMARK 500 ASN A 116 -134.03 -59.28 REMARK 500 LYS A 117 70.30 -25.63 REMARK 500 ASP A 119 -77.79 -42.76 REMARK 500 LEU A 120 -173.94 -52.84 REMARK 500 ALA A 121 -107.83 -88.96 REMARK 500 ALA A 122 -173.75 46.62 REMARK 500 ARG A 123 74.34 146.43 REMARK 500 THR A 144 -157.87 -122.83 REMARK 500 SER A 145 110.07 -161.97 REMARK 500 ARG A 149 28.21 42.55 REMARK 500 VAL A 152 -35.71 -39.30 REMARK 500 ILE A 163 -74.13 -77.50 REMARK 500 LEU A 168 -61.31 -100.70 REMARK 500 LYS A 170 -73.64 -21.34 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 41 0.29 SIDE CHAIN REMARK 500 ARG A 68 0.31 SIDE CHAIN REMARK 500 ARG A 73 0.20 SIDE CHAIN REMARK 500 ARG A 97 0.27 SIDE CHAIN REMARK 500 ARG A 102 0.12 SIDE CHAIN REMARK 500 ARG A 123 0.26 SIDE CHAIN REMARK 500 ARG A 128 0.25 SIDE CHAIN REMARK 500 ARG A 135 0.22 SIDE CHAIN REMARK 500 ARG A 149 0.30 SIDE CHAIN REMARK 500 ARG A 161 0.32 SIDE CHAIN REMARK 500 ARG A 164 0.31 SIDE CHAIN REMARK 500 ARG A 169 0.29 SIDE CHAIN 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 173 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 17 OG REMARK 620 2 TYR A 32 O 117.1 REMARK 620 3 ASP A 33 O 139.4 80.9 REMARK 620 4 GDP A 180 O1B 109.4 74.5 110.5 REMARK 620 5 GDP A 180 O2B 58.7 89.7 161.9 51.7 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 173 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDP A 180 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: TRT001000212.1 RELATED DB: TARGETDB DBREF 1AA9 A 1 171 UNP P01112 RASH_HUMAN 1 171 SEQRES 1 A 171 MET THR GLU TYR LYS LEU VAL VAL VAL GLY ALA GLY GLY SEQRES 2 A 171 VAL GLY LYS SER ALA LEU THR ILE GLN LEU ILE GLN ASN SEQRES 3 A 171 HIS PHE VAL ASP GLU TYR ASP PRO THR ILE GLU ASP SER SEQRES 4 A 171 TYR ARG LYS GLN VAL VAL ILE ASP GLY GLU THR CYS LEU SEQRES 5 A 171 LEU ASP ILE LEU ASP THR ALA GLY GLN GLU GLU TYR SER SEQRES 6 A 171 ALA MET ARG ASP GLN TYR MET ARG THR GLY GLU GLY PHE SEQRES 7 A 171 LEU CYS VAL PHE ALA ILE ASN ASN THR LYS SER PHE GLU SEQRES 8 A 171 ASP ILE HIS GLN TYR ARG GLU GLN ILE LYS ARG VAL LYS SEQRES 9 A 171 ASP SER ASP ASP VAL PRO MET VAL LEU VAL GLY ASN LYS SEQRES 10 A 171 CYS ASP LEU ALA ALA ARG THR VAL GLU SER ARG GLN ALA SEQRES 11 A 171 GLN ASP LEU ALA ARG SER TYR GLY ILE PRO TYR ILE GLU SEQRES 12 A 171 THR SER ALA LYS THR ARG GLN GLY VAL GLU ASP ALA PHE SEQRES 13 A 171 TYR THR LEU VAL ARG GLU ILE ARG GLN HIS LYS LEU ARG SEQRES 14 A 171 LYS LEU HET MG A 173 1 HET GDP A 180 40 HETNAM MG MAGNESIUM ION HETNAM GDP GUANOSINE-5'-DIPHOSPHATE FORMUL 2 MG MG 2+ FORMUL 3 GDP C10 H15 N5 O11 P2 HELIX 1 H1 LYS A 16 ILE A 24 1 9 HELIX 2 H2 ASP A 69 ARG A 73 1 5 HELIX 3 H3 GLU A 91 LYS A 104 1 14 HELIX 4 H4 GLU A 126 TYR A 137 1 12 HELIX 5 H5 VAL A 152 GLN A 165 1 14 SHEET 1 S1 6 SER A 39 ILE A 46 0 SHEET 2 S1 6 GLU A 49 ASP A 57 -1 O LEU A 53 N LYS A 42 SHEET 3 S1 6 THR A 2 VAL A 9 1 O LEU A 6 N LEU A 56 SHEET 4 S1 6 GLY A 77 ILE A 84 1 O LEU A 79 N VAL A 9 SHEET 5 S1 6 PRO A 110 LYS A 117 1 O VAL A 112 N CYS A 80 SHEET 6 S1 6 PRO A 140 THR A 144 1 O ILE A 142 N GLY A 115 LINK OG SER A 17 MG MG A 173 1555 1555 2.64 LINK O TYR A 32 MG MG A 173 1555 1555 3.10 LINK O ASP A 33 MG MG A 173 1555 1555 2.44 LINK MG MG A 173 O1B GDP A 180 1555 1555 2.80 LINK MG MG A 173 O2B GDP A 180 1555 1555 2.90 SITE 1 AC1 4 SER A 17 TYR A 32 ASP A 33 GDP A 180 SITE 1 AC2 13 GLY A 12 GLY A 13 GLY A 15 LYS A 16 SITE 2 AC2 13 SER A 17 PHE A 28 ASP A 30 TYR A 32 SITE 3 AC2 13 LYS A 117 SER A 145 ALA A 146 LYS A 147 SITE 4 AC2 13 MG A 173 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