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(-) Description

Title :  STRUCTURE OF FULLY MODIFIED FARNESYLATED INPP5E PEPTIDE IN COMPLEX WITH PDE6D
 
Authors :  E. K. Fansa, S. Isamil, A. Wittinghofer
Date :  02 Dec 15  (Deposition) - 13 Apr 16  (Release) - 20 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Lipid Binding Protein, Immunoglobulin-Like, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. K. Fansa, S. K. Koesling, E. Zent, A. Wittinghofer, S. Ismail
Pde6Delta-Mediated Sorting Of Inpp5E Into The Cilium Is Determined By Cargo-Carrier Affinity.
Nat Commun V. 7 11366 2016
PubMed-ID: 27063844  |  Reference-DOI: 10.1038/NCOMMS11366

(-) Compounds

Molecule 1 - RETINAL ROD RHODOPSIN-SENSITIVE CGMP 3',5'-CYCLIC PHOSPHODIESTERASE SUBUNIT DELTA
    Chains: A, 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
 
Molecule 2 - PHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE 5-PHOSPHATASE, S- FARNESYL-L-CYSTEINE METHYL ESTER
    Chains: C, D
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1CMT2Mod. ResidueO-METHYLCYSTEINE
2FAR2Ligand/IonFARNESYL
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1CMT1Mod. ResidueO-METHYLCYSTEINE
2FAR1Ligand/IonFARNESYL
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1CMT1Mod. ResidueO-METHYLCYSTEINE
2FAR1Ligand/IonFARNESYL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:53 , LEU A:54 , CYS A:56 , VAL A:80 , ALA A:111 , TYR A:149 , SER C:641 , THR C:642 , FAR C:702binding site for Di-peptide CMT C 701 and ILE C 643
2AC2SOFTWAREILE A:53 , CYS A:56 , GLN A:78 , ALA A:111 , THR A:131 , TYR A:149 , SER C:641 , ILE C:643binding site for residues CMT C 701 and FAR C 702
3AC3SOFTWAREILE B:53 , CYS B:56 , VAL B:59 , GLN B:78 , THR B:131 , SER D:641 , ILE D:643binding site for residues CMT D 701 and FAR D 702
4AC4SOFTWAREILE B:53 , LEU B:54 , CYS B:56 , VAL B:59 , TYR B:149 , SER D:641 , THR D:642 , FAR D:702binding site for Di-peptide CMT D 701 and ILE D 643

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5F2U)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5F2U)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5F2U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5F2U)

(-) Exons   (0, 0)

(no "Exon" information available for 5F2U)

(-) 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:149
                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhheeeeeeeeee.....eeeee.........eeeeeee.hhhhh.eeeeeeeeee...eeeeeeeeeeee..eeeeeeeeeeeee...eeeeeeeeee..hhhhh.hhhhhh..eeeeeeeee..eeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f2u A   2 SAKDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKAVSRELNFSSTEQMEKFRLEQKVYFKGQCLEEWFFEFGFVIPNSTNTWQSLIEAAPESQMMPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV 150
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141         


Chain B from PDB  Type:PROTEIN  Length:148
                                                                                                                                                                                    
               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
                 5f2u B   3 AKDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKAVSRELNFSSTEQMEKFRLEQKVYFKGQCLEEWFFEFGFVIPNSTNTWQSLIEAAPESQMMPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV 150
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142        


Chain C from PDB  Type:PROTEIN  Length:4
                                    
               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
                 5f2u C 640 SSTI 643


Chain D from PDB  Type:PROTEIN  Length:4
                                    
               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
                 5f2u D 640 SSTI 643
   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 5F2U)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5F2U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5F2U)

(-) Gene Ontology  (14, 14)

Asymmetric 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 4jv6 4jv8 4jvb 4jvf 5e80 5e8f 5ml2 5ml3 5ml4 5ml6 5ml8 5nal 5tar 5tb5

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5F2U)