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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN KRAS G12D MUTANT IN COMPLEX WITH GDP
 
Authors :  T. Tran, A. Kaplan, B. R. Stockwell, L. Tong
Date :  13 Feb 17  (Deposition) - 22 Mar 17  (Release) - 22 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.83
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Kras, Gtpase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. E. Welsch, A. Kaplan, J. M. Chambers, M. E. Stokes, P. H. Bos, A. Zask, Y. Zhang, M. Sanchez-Martin, M. A. Badgley, C. S. Huang, T. H. Tran, H. Akkiraju, L. M. Brown, R. Nandakumar, S. Cremers, W. S. Yang, L. Tong K. P. Olive, A. Ferrando, B. R. Stockwell
Multivalent Small-Molecule Pan-Ras Inhibitors.
Cell V. 168 878 2017
PubMed-ID: 28235199  |  Reference-DOI: 10.1016/J.CELL.2017.02.006

(-) Compounds

Molecule 1 - GTPASE KRAS
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: KRAS, KRAS2, RASK2
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: K-RAS 2, KI-RAS, C-K-RAS, C-KI-RAS

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1GDP2Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2GOL2Ligand/IonGLYCEROL
3MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2GOL1Ligand/IonGLYCEROL
3MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2GOL1Ligand/IonGLYCEROL
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:13 , VAL A:14 , GLY A:15 , LYS A:16 , SER A:17 , ALA A:18 , PHE A:28 , ASP A:30 , ASN A:116 , LYS A:117 , ASP A:119 , LEU A:120 , SER A:145 , ALA A:146 , LYS A:147 , MG A:202 , HOH A:310 , HOH A:312 , HOH A:324 , HOH A:344 , HOH A:379 , HOH A:403binding site for residue GDP A 201
2AC2SOFTWARESER A:17 , GDP A:201 , HOH A:310 , HOH A:312 , HOH A:327 , HOH A:338binding site for residue MG A 202
3AC3SOFTWAREASN A:85 , GLU A:91 , LEU A:120 , PRO A:121 , SER A:122 , LEU A:133 , HOH A:340binding site for residue GOL A 203
4AC4SOFTWAREGLY B:13 , VAL B:14 , GLY B:15 , LYS B:16 , SER B:17 , ALA B:18 , PHE B:28 , ASP B:30 , ASN B:116 , LYS B:117 , ASP B:119 , LEU B:120 , SER B:145 , ALA B:146 , LYS B:147 , MG B:202 , HOH B:314 , HOH B:322 , HOH B:343 , HOH B:344 , HOH B:372 , HOH B:394binding site for residue GDP B 201
5AC5SOFTWARESER B:17 , GDP B:201 , HOH B:314 , HOH B:324 , HOH B:333 , HOH B:344binding site for residue MG B 202
6AC6SOFTWAREASN B:85 , GLU B:91 , PRO B:121 , SER B:122 , LEU B:133 , HOH B:328binding site for residue GOL B 203

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5US4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5US4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5US4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5US4)

(-) Exons   (0, 0)

(no "Exon" information available for 5US4)

(-) Sequences/Alignments

Asymmetric 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    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:164
                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.....hhhhhhhhhhhh...........eeeeeeeee..eeeeeeeee...hhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeee.........hhhhhhhhhhhhh..eee.......hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5us4 A   1 MTEYKLVVVGADGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTASAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK 169
                                    10        20        30        40        50        65        75        85        95       105       115       125       135       145       155       165    
                                                                                     59|                                                                                                        
                                                                                      65                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:162
                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee.....hhhhhhhhhhhh...........eeeeeeeee..eeeeeeeee...hhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeee.........hhhhhhhhhhhhh..eee.......hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5us4 B   1 MTEYKLVVVGADGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK 169
                                    10        20        30        40        50        67        77        87        97       107       117       127       137       147       157       167  
                                                                                     59|                                                                                                      
                                                                                      67
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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  (0, 0)

(no "SCOP Domain" information available for 5US4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5US4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5US4)

(-) Gene Ontology  (49, 49)

Asymmetric Unit(hide GO term definitions)

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  5us4
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  RASK_HUMAN | P01116
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 Related Entries

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

UniProtKB/Swiss-Prot
        RASK_HUMAN | P01116: 1d8d 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 4lyj 4m1o 4m1s 4m1t 4m1w 4m1y 4m21 4m22 4nmm 4obe 4pzy 4pzz 4q01 4q02 4q03 4ql3 4tq9 4tqa 4wa7 5f2e 5kyk 5tar 5tb5 5uqw 5usj 5v6s 5v6v 5xco

(-) Related Entries Specified in the PDB File

5uqw 5usj