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(-) Description

Title :  THE CRYSTAL STRUCTURE OF PDE6D IN COMPLEX TO INHIBITOR-1
 
Authors :  Z. Gunther, B. Papke, S. Ismail, N. Vartak, A. Chandra, M. Hoffmann, S. H G. Triola, A. Wittinghofer, P. Bastiaens, H. Waldmann
Date :  25 Mar 13  (Deposition) - 22 May 13  (Release) - 05 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.87
Chains :  Asym./Biol. Unit :  B
Keywords :  Immunoglobulin-Like Beta-Sandwich, Gdi-Like Solubilizing Factor, Prenyl Binding Protein, Protein Binding-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Zimmermann, B. Papke, S. Ismail, N. Vartak, A. Chandra, M. Hoffmann S. A. Hahn, G. Triola, A. Wittinghofer, P. I. Bastiaens, H. Waldmann
Small Molecule Inhibition Of The Kras Pded Interaction Impairs Oncogenic Kras Signalling
Nature V. 497 638 2013
PubMed-ID: 23698361  |  Reference-DOI: 10.1038/NATURE12205

(-) Compounds

Molecule 1 - RETINAL ROD RHODOPSIN-SENSITIVE CGMP 3',5'-CYCLIC PHOSPHODIESTERASE SUBUNIT DELTA
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PDE6D, PDED
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: GMP-PDE DELTA, PROTEIN P17

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
118F2Ligand/Ion1-BENZYL-2-PHENYL-1H-BENZIMIDAZOLE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET B:20 , TRP B:32 , ALA B:47 , ARG B:61 , GLN B:78BINDING SITE FOR RESIDUE 18F B 201
2AC2SOFTWARELEU B:22 , ILE B:53 , LEU B:54 , CYS B:56 , GLU B:88 , ILE B:109 , ALA B:111 , MET B:117 , LEU B:147 , TYR B:149BINDING SITE FOR RESIDUE 18F B 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4JV6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4JV6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4JV6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4JV6)

(-) Exons   (0, 0)

(no "Exon" information available for 4JV6)

(-) 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    
   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 B from PDB  Type:PROTEIN  Length:146
                                                                                                                                                                                  
               SCOP domains d4jv6b_ B: GMP-PDE delta                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhheeeeeeeeee....eeeee.........eeeeeee.hhhhh.eeeeeeeeee...eeeeeeeeeeee..eeeeeeeeeeeee...eeeeeeeeee......hhhhhh..eeeeeeeee..eeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jv6 B   2 SAKDERAREILRGFKLNWMNLRDATGKILWQGTEDLSVPGVEHEARVPKKILKCKAVSRELNFSSTEQMEKFRLEQKVYFKGQCLEEWFFEFGFVIPNSTNTWQSLIEAASQMMPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV 150
                                    11        21   ||   32        42        52        62        72        82        92       102       112|      124       134       144      
                                                  25|                                                                                  112|                                   
                                                   27                                                                                   115
   Legend:   → Mismatch (orange background)
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  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
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4JV6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4JV6)

(-) Gene Ontology  (14, 14)

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
        PDE6D_HUMAN | O43924: 1ksg 1ksh 1ksj 3t5g 3t5i 4jhp 4jv8 4jvb 4jvf 5e80 5e8f 5f2u 5ml2 5ml3 5ml4 5ml6 5ml8 5nal 5tar 5tb5

(-) Related Entries Specified in the PDB File

4jv8 4jvb 4jvf