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(-) Description

Title :  CRYSTAL STRUCTURE OF SMALL MOLECULE VINYLSULFONAMIDE 9 COVALENTLY BOUND TO K-RAS G12C, ALTERNATIVE SPACE GROUP
 
Authors :  J. M. Ostrem, U. Peters, M. L. Sos, J. A. Wells, K. M. Shokat
Date :  31 Jul 13  (Deposition) - 27 Nov 13  (Release) - 18 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.93
Chains :  Asym./Biol. Unit :  A
Keywords :  Gtpase, Gdp Bound, Small Molecule Inhibitor, Covalent Binder, Signaling Protein-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. M. Ostrem, U. Peters, M. L. Sos, J. A. Wells, K. M. Shokat
K-Ras(G12C) Inhibitors Allosterically Control Gtp Affinity And Effector Interactions.
Nature V. 503 548 2013
PubMed-ID: 24256730  |  Reference-DOI: 10.1038/NATURE12796

(-) Compounds

Molecule 1 - GTPASE KRAS
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPJEXPRESS411
    Expression System StrainBL21 (DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 1-169
    GeneKRAS, KRAS ISOFORM 2B, KRAS2, RASK2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymK-RAS 2, KI-RAS, C-K-RAS, C-KI-RAS, GTPASE KRAS, N- TERMINALLY PROCESSED

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
121F1Ligand/IonN-{1-[N-(4-CHLORO-5-IODO-2-METHOXYPHENYL)GLYCYL]PIPERIDIN-4-YL}ETHANESULFONAMIDE
2GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
3MG1Ligand/IonMAGNESIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:17 , TYR A:32 , GDP A:203 , HOH A:312 , HOH A:360BINDING SITE FOR RESIDUE MG A 201
2AC2SOFTWAREVAL A:9 , GLY A:10 , CYS A:12 , THR A:58 , GLU A:62 , GLU A:63 , ARG A:68 , TYR A:71 , MET A:72 , TYR A:96 , GLN A:99 , HOH A:362BINDING SITE FOR RESIDUE 21F A 202
3AC3SOFTWAREALA A:11 , GLY A:13 , VAL A:14 , GLY A:15 , LYS A:16 , SER A:17 , ALA A:18 , PHE A:28 , VAL A:29 , ASP A:30 , TYR A:32 , ASN A:116 , LYS A:117 , ASP A:119 , LEU A:120 , SER A:145 , ALA A:146 , LYS A:147 , MG A:201 , HOH A:307 , HOH A:322 , HOH A:330 , HOH A:335 , HOH A:350 , HOH A:374BINDING SITE FOR RESIDUE GDP A 203

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4LYJ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4LYJ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4LYJ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4LYJ)

(-) Exons   (0, 0)

(no "Exon" information available for 4LYJ)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:166
                                                                                                                                                                                                      
               SCOP domains d4lyja_ A: automated matches                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee....hhhhhhhhhhhh............eeeeeeee..eeeeeeee...hhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhh......eeeeee.........hhhhhhhhhhhhh..eee.......hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lyj A   2 TEYKLVVVGACGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETSLLDILDTAGQEEYSAMRDQYMRTGEGFLLVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKSDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHK 167
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161      

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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4LYJ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4LYJ)

(-) Gene Ontology  (49, 49)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        RASK_HUMAN | P011161d8d 1d8e 1kzo 1kzp 1n4p 1n4q 1n4r 1n4s 3gft 4dsn 4dso 4dst 4dsu 4epr 4ept 4epv 4epw 4epx 4epy 4l8g 4ldj 4lpk 4lrw 4luc 4lv6 4lyf 4lyh 4m1o 4m1s 4m1t 4m1w 4m1y 4m21 4m22 4nmm 4obe 4pzy 4pzz 4q01 4q02 4q03 4ql3 4tq9 4tqa 4wa7 5f2e 5kyk 5tar 5tb5 5uqw 5us4 5usj 5v6s 5v6v 5xco

(-) Related Entries Specified in the PDB File

4l8g RELATED MUTANT OF PROTEIN
4l9s PROTEIN ISOFORM
4l9w PROTEIN ISOFORM
4lpk WILD-TYPE FORM OF PROTEIN
4lrw PROTEIN WITHOUT INHIBITOR BOUND
4luc PROTEIN BOUND TO RELATED COMPOUND
4lv6 PROTEIN BOUND TO RELATED COMPOUND
4lyf PROTEIN BOUND TO RELATED COMPOUND
4lyh PROTEIN BOUND TO SAME COMPOUND, DIFFERENT SPACE GROUP
4m1o RELATED COMPOUND BOUND TO PROTEIN
4m1s RELATED COMPOUND BOUND TO PROTEIN
4m1t RELATED COMPOUND BOUND TO PROTEIN
4m1w RELATED COMPOUND BOUND TO PROTEIN
4m1y RELATED COMPOUND BOUND TO PROTEIN
4m21 RELATED COMPOUND BOUND TO PROTEIN
4m22 RELATED COMPOUND BOUND TO PROTEIN