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(-) Description

Title :  SECOND-SITE SCREENING OF K-RAS IN THE PRESENCE OF COVALENTLY ATTACHED FIRST-SITE LIGANDS
 
Authors :  Q. Sun, J. Phan, A. Friberg, D. V. Camper, E. T. Olejniczak, S. W. Fesik
Date :  31 Mar 14  (Deposition) - 10 Sep 14  (Release) - 10 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.88
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  B  (1x)
Keywords :  Small Gtpase, Signaling Transduction, Sos, Raf, Cytosol, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Q. Sun, J. Phan, A. R. Friberg, D. V. Camper, E. T. Olejniczak, S. W. Fesi
A Method For The Second-Site Screening Of K-Ras In The Presence Of A Covalently Attached First-Site Ligand.
J. Biomol. Nmr V. 60 11 2014
PubMed-ID: 25087006  |  Reference-DOI: 10.1007/S10858-014-9849-8

(-) Compounds

Molecule 1 - K-RAS
    Chains: A, B
    EC Number: 3.6.5.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (1x): A 
Biological Unit 3 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
12XR2Ligand/Ion2-CHLORO-1-(1H-INDOL-3-YL)ETHANONE
2GDP2Ligand/IonGUANOSINE-5'-DIPHOSPHATE
3MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
12XR2Ligand/Ion2-CHLORO-1-(1H-INDOL-3-YL)ETHANONE
2GDP2Ligand/IonGUANOSINE-5'-DIPHOSPHATE
3MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
12XR-1Ligand/Ion2-CHLORO-1-(1H-INDOL-3-YL)ETHANONE
2GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
3MG-1Ligand/IonMAGNESIUM ION
Biological Unit 3 (2, 3)
No.NameCountTypeFull Name
12XR2Ligand/Ion2-CHLORO-1-(1H-INDOL-3-YL)ETHANONE
2GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
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 , VAL A:29 , ASP A:30 , ASN A:116 , LYS A:117 , ASP A:119 , LEU A:120 , ASP A:132 , SER A:145 , ALA A:146 , LYS A:147 , MG A:202 , HOH A:301 , HOH A:318 , HOH A:357 , HOH A:358 , HOH A:359 , HOH A:362 , HOH A:373 , HOH A:383BINDING SITE FOR RESIDUE GDP A 201
2AC2SOFTWARESER A:17 , GDP A:201 , HOH A:301 , HOH A:302 , HOH A:304 , HOH A:357BINDING SITE FOR RESIDUE MG A 202
3AC3SOFTWAREGLY 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:327 , HOH B:345 , HOH B:352 , HOH B:371 , HOH B:380 , HOH B:464BINDING SITE FOR RESIDUE GDP B 201
4AC4SOFTWARESER B:17 , GDP B:201 , HOH B:301 , HOH B:306 , HOH B:314 , HOH B:464BINDING SITE FOR RESIDUE MG B 202
5AC5SOFTWARECYS A:70 , THR A:74 , LEU B:6 , VAL B:7 , SER B:39 , ASP B:54 , TYR B:71 , THR B:74 , HOH B:379BINDING SITE FOR RESIDUE 2XR B 203
6AC6SOFTWARELYS A:5 , LEU A:6 , VAL A:7 , SER A:39 , ASP A:54 , CYS B:70 , ARG B:73BINDING SITE FOR RESIDUE 2XR B 204

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:0 -Met A:1
2Ala B:59 -Gly B:60

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4PZY)

(-) 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:170
                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee....hhhhhhhhhhhh...........eeeeeeeee..eeeeeeeee.......hhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeee.........hhhhhhhhhhhhh..eee.......hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pzy A   0 GMTEYKLVVVGAVGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDCYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKSDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK 169
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169


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...........eeeeeeeee..eeeeeeeee.......hhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeee.........hhhhhhhhhhhhh..eee.......hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pzy B   0 GMTEYKLVVVGAVGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDCYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKSDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK 169
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169
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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 4PZY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (49, 49)

Asymmetric Unit(hide GO term definitions)

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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 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

4pzz 4q01 4q02 4q03