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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN KRAS G12D MUTANT IN COMPLEX WITH GDPNP
 
Authors :  C. S. Huang, 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 :  1.94
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  E  (1x)
Biol. Unit 6:  F  (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
    ChainsA, B, C, D, E, F
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15B
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneKRAS, KRAS2, RASK2
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymK-RAS 2, KI-RAS, C-K-RAS, C-KI-RAS

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (1x)A     
Biological Unit 2 (1x) B    
Biological Unit 3 (1x)  C   
Biological Unit 4 (1x)   D  
Biological Unit 5 (1x)    E 
Biological Unit 6 (1x)     F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
1GNP6Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MG6Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 5 (1, 1)
No.NameCountTypeFull Name
1GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 6 (1, 1)
No.NameCountTypeFull Name
1GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:17 , THR A:35 , GNP A:1002 , HOH A:1104 , HOH A:1131binding site for residue MG A 1001
02AC2SOFTWAREASP A:12 , 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 , PRO A:34 , THR A:35 , GLY A:60 , ASN A:116 , LYS A:117 , ASP A:119 , LEU A:120 , SER A:145 , ALA A:146 , LYS A:147 , MG A:1001 , HOH A:1104 , HOH A:1131 , HOH A:1140 , HOH A:1142 , HOH A:1147 , HOH A:1203binding site for residue GNP A 1002
03AC3SOFTWARESER B:17 , THR B:35 , GNP B:1002 , HOH B:1117 , HOH B:1121binding site for residue MG B 1001
04AC4SOFTWAREASP B:12 , GLY B:13 , VAL B:14 , GLY B:15 , LYS B:16 , SER B:17 , ALA B:18 , PHE B:28 , VAL B:29 , ASP B:30 , TYR B:32 , PRO B:34 , THR B:35 , GLY B:60 , ASN B:116 , LYS B:117 , ASP B:119 , LEU B:120 , SER B:145 , ALA B:146 , LYS B:147 , MG B:1001 , HOH B:1110 , HOH B:1117 , HOH B:1121 , HOH B:1172 , HOH B:1179binding site for residue GNP B 1002
05AC5SOFTWARESER C:17 , THR C:35 , GNP C:1002 , HOH C:1103 , HOH C:1123binding site for residue MG C 1001
06AC6SOFTWAREASP C:12 , GLY C:13 , VAL C:14 , GLY C:15 , LYS C:16 , SER C:17 , ALA C:18 , PHE C:28 , VAL C:29 , ASP C:30 , TYR C:32 , PRO C:34 , THR C:35 , GLY C:60 , ASN C:116 , LYS C:117 , ASP C:119 , LEU C:120 , SER C:145 , ALA C:146 , LYS C:147 , MG C:1001 , HOH C:1103 , HOH C:1123 , HOH C:1140 , HOH C:1166binding site for residue GNP C 1002
07AC7SOFTWARESER D:17 , THR D:35 , GNP D:1002 , HOH D:1137 , HOH D:1138binding site for residue MG D 1001
08AC8SOFTWAREASP D:12 , GLY D:13 , VAL D:14 , GLY D:15 , LYS D:16 , SER D:17 , ALA D:18 , PHE D:28 , VAL D:29 , ASP D:30 , GLU D:31 , TYR D:32 , PRO D:34 , THR D:35 , GLY D:60 , ASN D:116 , LYS D:117 , ASP D:119 , LEU D:120 , SER D:145 , ALA D:146 , LYS D:147 , MG D:1001 , HOH D:1129 , HOH D:1133 , HOH D:1137 , HOH D:1138 , HOH D:1149 , HOH D:1183binding site for residue GNP D 1002
09AC9SOFTWARESER E:17 , THR E:35 , GNP E:1002 , HOH E:1111 , HOH E:1123binding site for residue MG E 1001
10AD1SOFTWAREASP E:12 , GLY E:13 , VAL E:14 , GLY E:15 , LYS E:16 , SER E:17 , ALA E:18 , PHE E:28 , VAL E:29 , ASP E:30 , GLU E:31 , PRO E:34 , THR E:35 , GLY E:60 , ASN E:116 , LYS E:117 , ASP E:119 , LEU E:120 , SER E:145 , ALA E:146 , LYS E:147 , MG E:1001 , HOH E:1111 , HOH E:1123 , HOH E:1125 , HOH E:1138 , HOH E:1151 , HOH E:1167 , HOH E:1170 , HOH E:1180binding site for residue GNP E 1002
11AD2SOFTWARESER F:17 , THR F:35 , GNP F:1002 , HOH F:1110 , HOH F:1118binding site for residue MG F 1001
12AD3SOFTWAREASP F:12 , GLY F:13 , VAL F:14 , GLY F:15 , LYS F:16 , SER F:17 , ALA F:18 , PHE F:28 , VAL F:29 , ASP F:30 , PRO F:34 , THR F:35 , GLY F:60 , ASN F:116 , LYS F:117 , ASP F:119 , LEU F:120 , SER F:145 , ALA F:146 , LYS F:147 , MG F:1001 , HOH F:1110 , HOH F:1118 , HOH F:1126 , HOH F:1151 , HOH F:1157 , HOH F:1174binding site for residue GNP F 1002

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5USJ)

(-) 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:168
                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeeeee....hhhhhhhhhhhh..........eeeeeeeeee..eeeeeeeeee...hhhhhhhhhh..eeeeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeee.........hhhhhhhhhhhhh..eee.......hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5usj A  -2 GSHMTEYKLVVVGADGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKE 168
                                     7        17        27        37        47        57  ||    70        80        90       100       110       120       130       140       150       160        
                                                                                         60|                                                                                                        
                                                                                          64                                                                                                        

Chain B from PDB  Type:PROTEIN  Length:170
                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee....hhhhhhhhhhhh..........eeeeeeeeee..eeeeeeeeee..hhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeee.........hhhhhhhhhhhhh..eee.......hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5usj B  -2 GSHMTEYKLVVVGADGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHK 167
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167

Chain C from PDB  Type:PROTEIN  Length:171
                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeee.....hhhhhhhhhhhh..........eeeeeeeeee..eeeeeeeeee..hhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeee.........hhhhhhhhhhhhh..eee.......hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5usj C  -3 RGSHMTEYKLVVVGADGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHK 167
                                     6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166 

Chain D from PDB  Type:PROTEIN  Length:162
                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeee.....hhhhhhhhhhhh..........eeeeeeeeee..eeeeeeeeee...hhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeee.........hhhhhhhhhhhh...eee.......hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5usj D  -1 SHMTEYKLVVVGADGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHK 167
                                     8        18        28        38        48        58 ||     75        85        95       105       115       125       135       145       155       165  
                                                                                        60|                                                                                                   
                                                                                         68                                                                                                   

Chain E from PDB  Type:PROTEIN  Length:169
                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeee....hhhhhhhhhhhh..........eeeeeeeeee..eeeeeeeeee..hhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeee.........hhhhhhhhhhhhh..eee.......hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5usj E  -2 GSHMTEYKLVVVGADGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKH 166
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157         

Chain F from PDB  Type:PROTEIN  Length:170
                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeee.....hhhhhhhhhhhh..........eeeeeeeeee..eeeeeeeeee.....hhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhh......eeeeee.........hhhhhhhhhhhhh..eee.......hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5usj F  -3 RGSHMTEYKLVVVGADGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKH 166
                                     6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166

   Legend:   → Mismatch (orange background)
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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 5USJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (49, 49)

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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 4lyj 4m1o 4m1s 4m1t 4m1w 4m1y 4m21 4m22 4nmm 4obe 4pzy 4pzz 4q01 4q02 4q03 4ql3 4tq9 4tqa 4wa7 5f2e 5kyk 5tar 5tb5 5uqw 5us4 5v6s 5v6v 5xco

(-) Related Entries Specified in the PDB File

5uqw 5us4