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(-) Description

Title :  STRUCTURE OF FULLY MODIFIED GERANYLGERANYLATED PDE6C PEPTIDE IN COMPLEX WITH PDE6D
 
Authors :  E. K. Fansa, N. J. O'Reilly, S. A. Ismail, A. Wittinghofer
Date :  14 Oct 15  (Deposition) - 18 Nov 15  (Release) - 16 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,C,D,E
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  C,E  (1x)
Keywords :  Prenyl Binding Protein, Immunoglobulin-Like Beta Sandwitch Fold, Geranylgeranyl, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. K. Fansa, N. J. O'Reilly, S. Ismail, A. Wittinghofer
The N- And C-Terminal Ends Of Rpgr Can Bind To Pde6 Delta.
Embo Rep. V. 16 1583 2015
PubMed-ID: 26553937  |  Reference-DOI: 10.15252/EMBR.201541404

(-) Compounds

Molecule 1 - RETINAL ROD RHODOPSIN-SENSITIVE CGMP 3',5'-CYCLIC PHOSPHODIESTERASE SUBUNIT DELTA
    Chains: A, C
    EC Number: 3.1.4.35
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 2-150
    Gene: PDE6D, PDED
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: GMP-PDE DELTA,PROTEIN P17
 
Molecule 2 - CONE CGMP-SPECIFIC 3',5'-CYCLIC PHOSPHODIESTERASE SUBUNIT ALPHA'
    Chains: D, E
    EC Number: 3.1.4.35
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 851-855
    Gene: PDE6C, PDEA2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CGMP PHOSPHODIESTERASE 6C

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ACDE
Biological Unit 1 (1x): A D 
Biological Unit 2 (1x):  C E

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1CMT2Mod. Amino AcidO-METHYLCYSTEINE
2GER2Ligand/IonGERAN-8-YL GERAN
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1CMT1Mod. Amino AcidO-METHYLCYSTEINE
2GER1Ligand/IonGERAN-8-YL GERAN
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1CMT1Mod. Amino AcidO-METHYLCYSTEINE
2GER1Ligand/IonGERAN-8-YL GERAN

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:20 , SER A:39 , GLN A:78 , ILE A:129 , THR A:131 , PHE A:133 , CMT D:855binding site for residue GER D 901
2AC2SOFTWARESER C:39 , GLN C:78 , ILE C:129 , CMT E:855binding site for residue GER E 901

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5E8F)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5E8F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5E8F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5E8F)

(-) Exons   (0, 0)

(no "Exon" information available for 5E8F)

(-) 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:147
                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhheeeeeeeeee.....eeeee.........eeeeeee.hhhhh.eeeeeeeeee...eeeeeeeeeeee..eeeeeeeeeeeee...eeeeeeeeee..hhhhh.hhhhhh..eeeeeeeee..eeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5e8f A   4 KDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKAVSRELNFSSTEQMEKFRLEQKVYFKGQCLEEWFFEFGFVIPNSTNTWQSLIEAAPESQMMPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV 150
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       


Chain C from PDB  Type:PROTEIN  Length:149
                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhheeeeeeeeee.....eeeee.........eeeeeee.hhhhh.eeeeeeeeee...eeeeeeeeeeee..eeeeeeeeeeeee...eeeeeeeeee..hhhhh.hhhhhh..eeeeeeeee..eeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5e8f C   2 SAKDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKAVSRELNFSSTEQMEKFRLEQKVYFKGQCLEEWFFEFGFVIPNSTNTWQSLIEAAPESQMMPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV 150
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141         


Chain D from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..... Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 5e8f D 851 KSKTc 855
                                |
                              855-CMT


Chain E from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..... Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 5e8f E 851 KSKTc 855
                                |
                                |
                              855-CMT
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 5E8F)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5E8F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5E8F)

(-) Gene Ontology  (25, 29)

Asymmetric Unit(hide GO term definitions)

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  5e8f
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  PDE6C_HUMAN | P51160
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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
        PDE6C_HUMAN | P51160: 3jwq 3jwr
        PDE6D_HUMAN | O43924: 1ksg 1ksh 1ksj 3t5g 3t5i 4jhp 4jv6 4jv8 4jvb 4jvf 5e80 5f2u 5ml2 5ml3 5ml4 5ml6 5ml8 5nal 5tar 5tb5

(-) Related Entries Specified in the PDB File

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