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(-) Description

Title :  THE CRYSTAL STRUCTURE OF INHIBITOR-15 COVALENTLY BOUND TO PDE6D
 
Authors :  E. K. Fansa, P. Martin-Gago, H. Waldmann, A. Wittinghofer
Date :  28 Feb 17  (Deposition) - 10 May 17  (Release) - 31 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  B
Keywords :  Lipid Binding Protein, Woodward'S Reagent K, Covalent Protein Labeling At Glutamic Acids, Arl2 Mediated Cargo Release (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Martin-Gago, E. K. Fansa, M. Winzker, S. Murarka, P. Janning, C. Schultz-Fademrecht, M. Baumann, A. Wittinghofer, H. Waldmann
Covalent Protein Labeling At Glutamic Acids.
Cell Chem Biol V. 24 589 2017
PubMed-ID: 28434875  |  Reference-DOI: 10.1016/J.CHEMBIOL.2017.03.015

(-) 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, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
18RQ1Ligand/Ion~{N}4-[(4-CHLOROPHENYL)METHYL]-~{N}1-(CYCLOHEXYLMETHYL)-~{N}4-CYCLOPENTYL-~{N}1-[(~{Z})-4-[(~{E})-METHYLIMINOMETHYL]-5-OXIDANYL-HEX-4-ENYL]BENZENE-1,4-DISULFONAMIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU B:17 , MET B:20 , LEU B:22 , VAL B:49 , ILE B:53 , CYS B:56 , ARG B:61 , GLN B:78 , VAL B:80 , LEU B:87 , GLU B:88 , TRP B:90 , ILE B:109 , ALA B:111 , SER B:115 , MET B:117 , VAL B:127 , THR B:131 , PHE B:133 , LEU B:147 , TYR B:149binding site for residue 8RQ B 201

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5NAL)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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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:150
                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------ 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
                 5nal B   1 MSAKDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKAVSRELNFSSTEQMEKFRLEQKVYFKGQCLEEWFFEFGFVIPNSTNTWQSLIEAAPESQMMPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV 150
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150
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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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)

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  5nal
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  PDE6D_HUMAN | O43924
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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 4jv6 4jv8 4jvb 4jvf 5e80 5e8f 5f2u 5ml2 5ml3 5ml4 5ml6 5ml8 5tar 5tb5

(-) Related Entries Specified in the PDB File

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