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(-) Description

Title :  CRYSTAL STRUCTURE OF RPE65 IN COMPLEX WITH MB-008 AND PALMITATE
 
Authors :  P. D. Kiser, K. Palczewski
Date :  24 Jan 17  (Deposition) - 17 May 17  (Release) - 21 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Retinoid Isomerase, Non-Heme Iron Enzyme, Inhibitor, Isomerase, Isomerase-Isomerase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. D. Kiser, J. Zhang, M. Badiee, J. Kinoshita, N. S. Peachey, G. P. Tochtrop, K. Palczewski
Rational Tuning Of Visual Cycle Modulator Pharmacodynamics.
J. Pharmacol. Exp. Ther. V. 362 131 2017
PubMed-ID: 28476927  |  Reference-DOI: 10.1124/JPET.117.240721

(-) Compounds

Molecule 1 - RETINOID ISOMEROHYDROLASE
    Chains: A, B
    EC Number: 3.1.1.64
    Organism Common: BOVINE
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913
    Synonym: ALL-TRANS-RETINYL-PALMITATE HYDROLASE,RETINAL PIGMENT EPITHELIUM-SPECIFIC 65 KDA PROTEIN,RETINOL ISOMERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 10)

Asymmetric/Biological Unit (5, 10)
No.NameCountTypeFull Name
18E42Ligand/Ion(3S)-3-({3-[(1R)-3-AMINO-1-HYDROXYPROPYL]PHENOXY}METHYL)HEXAN-1-OL
2FE22Ligand/IonFE (II) ION
3NA2Ligand/IonSODIUM ION
4PG42Ligand/IonTETRAETHYLENE GLYCOL
5PLM2Ligand/IonPALMITIC ACID

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:180 , HIS A:241 , HIS A:313 , HIS A:527 , PLM A:602binding site for residue FE2 A 601
02AC2SOFTWARELEU A:60 , VAL A:134 , HIS A:180 , HIS A:241 , TYR A:338 , LEU A:341 , PHE A:418 , PHE A:442 , PRO A:444 , VAL A:524 , HIS A:527 , FE2 A:601 , 8E4 A:603binding site for residue PLM A 602
03AC3SOFTWAREPHE A:61 , PHE A:103 , VAL A:134 , THR A:147 , GLU A:148 , ASN A:194 , PHE A:279 , TYR A:338 , PLM A:602binding site for residue 8E4 A 603
04AC4SOFTWAREGLN A:4 , VAL A:459 , TRP A:460 , GLN A:461 , PRO A:463 , NA A:605 , HOH A:842binding site for residue PG4 A 604
05AC5SOFTWAREGLN A:461 , PG4 A:604 , HOH A:842binding site for residue NA A 605
06AC6SOFTWAREHIS B:180 , HIS B:241 , HIS B:313 , HIS B:527 , PLM B:602binding site for residue FE2 B 601
07AC7SOFTWARELEU B:60 , VAL B:134 , HIS B:180 , HIS B:241 , TYR B:338 , GLU B:417 , PHE B:418 , PHE B:442 , PRO B:444 , VAL B:524 , HIS B:527 , FE2 B:601 , 8E4 B:603binding site for residue PLM B 602
08AC8SOFTWAREPHE B:61 , PHE B:103 , VAL B:134 , THR B:147 , GLU B:148 , ASN B:194 , PHE B:279 , PLM B:602binding site for residue 8E4 B 603
09AC9SOFTWAREGLN B:4 , VAL B:459 , TRP B:460 , GLN B:461 , PRO B:463 , NA B:605 , HOH B:925binding site for residue PG4 B 604
10AD1SOFTWAREGLN B:461 , PG4 B:604 , HOH B:925binding site for residue NA B 605

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5ULG)

(-) 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 A from PDB  Type:PROTEIN  Length:506
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhh........eeeeeee.......eeeeeeeeee.ee..ee.......eeeeeeeeee..eeeeeeee..hhhhhhhhhhh.....................eeeee..eeeee....eeeee......eeeeee.hhh..........ee.....eeeeeee..eeeeeee........hhhhhheeeeeee.............ee...eeeeee..eeehhhhhhh...hhh.eee.....eeeeeee....eeeeeeeee..eeeeeeeeeeee..eeeeeeeeee...hhhhhhhhhhhh.hhhhhhhhhh...eeeeeeeeee...hhhhh............eeee....eeeee.eeee....eeeeeee.hhhhhh.....eeeeeeee..eeeeeeeee.....eeee..........eeee.........eeeeeeee........eeeeeee.....eeeeeee........eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ulg A   1 MSSQVEHPAGGYKKLFETVEELSSPLTAHVTGRIPLWLTGSLLRCGPGLFEVGSEPFYHLFDGQALLHKFDFKEGHVTYHRRFIRTDAYVRAMTEKRIVITEFGTCAFPEVTDNALVNIYPVGEDYYACTETNFITKVNPETLETIKQVDLCNYVSVNGATAHPHIENDGTVYNIGNCFIAYNIVKIPPLQADKEDPISKSEIVVQFPCSDRFKPSYVHSFGLTPNYIVFVETPVKINLFKFLSGANYMDCFESNETMGVWLHIADKKRKKYINNKYRTSPFNLFHHINTYEDHEFLIVDLCCWKGFEFVYNYLYLANLRENWEEVKKNARKAPQPEVRRYVLPLNIDKADTGKNLVTLPNTTATAILCSDETIWLEPEVLFSGPRQAFEFPQINYQKYGGKPYTYAYGLGLNHFVPDRLCKLNVKTKETWVWQEPDSYPSEPIFVSHPDALEEDDGVVLSVVVSPGAGQKPAYLLILNAKDLSEVARAEVEINIPVTFHGLFKKS 533
                                    10        20        30        40        50        60        70        80        90       100       127       137       147       157       167       177       187       202       212       222       232       242       252       262   ||  277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527      
                                                                                                                                      109|                                                                  196|                                                             266|                                                                                                                                                                                                                                                                     
                                                                                                                                       127                                                                   202                                                              272                                                                                                                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:506
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhh........eeeeeee.......eeeeeeeeee.ee..ee.......eeeeeeeeee..eeeeeeee..hhhhhhhhhhh.....................eeeee..eeeee....eeeee......eeeeee.hhh..........ee.....eeeeeee..eeeeeee........hhhhhheeeeeee.............ee...eeeeee..eeehhhhhhh...hhh.eee.....eeeeeee....eeeeeeeee..eeeeeeeeeeee..eeeeeeeeee...hhhhhhhhhhhh.hhhhhhhhhh...eeeeeeeeee...hhhhh............eeee....eeeee.eeee....eeeeeee.hhhhhh.....eeeeeeee..eeeeeeeee.....eeee..........eeee.........eeeeeeee........eeeeeee.....eeeeeee........eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ulg B   1 MSSQVEHPAGGYKKLFETVEELSSPLTAHVTGRIPLWLTGSLLRCGPGLFEVGSEPFYHLFDGQALLHKFDFKEGHVTYHRRFIRTDAYVRAMTEKRIVITEFGTCAFPEVTDNALVNIYPVGEDYYACTETNFITKVNPETLETIKQVDLCNYVSVNGATAHPHIENDGTVYNIGNCFIAYNIVKIPPLQADKEDPISKSEIVVQFPCSDRFKPSYVHSFGLTPNYIVFVETPVKINLFKFLSGANYMDCFESNETMGVWLHIADKKRKKYINNKYRTSPFNLFHHINTYEDHEFLIVDLCCWKGFEFVYNYLYLANLRENWEEVKKNARKAPQPEVRRYVLPLNIDKADTGKNLVTLPNTTATAILCSDETIWLEPEVLFSGPRQAFEFPQINYQKYGGKPYTYAYGLGLNHFVPDRLCKLNVKTKETWVWQEPDSYPSEPIFVSHPDALEEDDGVVLSVVVSPGAGQKPAYLLILNAKDLSEVARAEVEINIPVTFHGLFKKS 533
                                    10        20        30        40        50        60        70        80        90       100       127       137       147       157       167       177       187       202       212       222       232       242       252       262   ||  277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527      
                                                                                                                                      109|                                                                  196|                                                             266|                                                                                                                                                                                                                                                                     
                                                                                                                                       127                                                                   202                                                              272
   Legend:   → Mismatch (orange background)
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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 5ULG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (20, 20)

Asymmetric/Biological Unit(hide GO term definitions)

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  RPE65_BOVIN | Q28175
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 Related Entries

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        RPE65_BOVIN | Q28175: 3fsn 3kvc 4f2z 4f30 4f3a 4f3d 4rsc 4rse 4ryx 4ryy 4ryz 4zhk 5ul5

(-) Related Entries Specified in the PDB File

5ul5