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(-) Description

Title :  CRYSTAL STRUCTURE OF RPE65 IN COMPLEX WITH EMIXUSTAT AND PALMITATE, P6522 CRYSTAL FORM
 
Authors :  P. D. Kiser, K. Palczewski
Date :  17 Dec 14  (Deposition) - 27 May 15  (Release) - 27 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  7-Bladed Beta Propeller, Monotopic Membrane Protein, Non-Heme Iron Enzyme, Retinoid Isomerase, Isomerase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Zhang, P. D. Kiser, M. Badiee, G. Palczewska, M. Golczak, G. P. Tochtrop, K. Palczewski
The Janus Face Of Primary Amine Compounds In Visual Cycle Modulation
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - RETINOID ISOMEROHYDROLASE
    Chains: A
    EC Number: 3.1.1.64
    Organism Common: BOVINE,COW,DOMESTIC CATTLE,DOMESTIC COW
    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

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 7)

Asymmetric Unit (5, 7)
No.NameCountTypeFull Name
1A3V1Ligand/Ion(1R)-3-AMINO-1-[3-(CYCLOHEXYLMETHOXY)PHENYL]PROPAN-1-OL
2FE21Ligand/IonFE (II) ION
3MPD3Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
4PLM1Ligand/IonPALMITIC ACID
5SO41Ligand/IonSULFATE ION
Biological Unit 1 (5, 14)
No.NameCountTypeFull Name
1A3V2Ligand/Ion(1R)-3-AMINO-1-[3-(CYCLOHEXYLMETHOXY)PHENYL]PROPAN-1-OL
2FE22Ligand/IonFE (II) ION
3MPD6Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
4PLM2Ligand/IonPALMITIC ACID
5SO42Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:180 , HIS A:241 , HIS A:313 , HIS A:527 , PLM A:602BINDING SITE FOR RESIDUE FE2 A 601
2AC2SOFTWAREVAL A:134 , HIS A:180 , HIS A:241 , TYR A:338 , PHE A:418 , LEU A:439 , PHE A:442 , HIS A:527 , FE2 A:601 , A3V A:603 , HOH A:846BINDING SITE FOR RESIDUE PLM A 602
3AC3SOFTWAREPHE A:61 , PHE A:103 , VAL A:134 , THR A:147 , GLU A:148 , PLM A:602 , HOH A:975BINDING SITE FOR RESIDUE A3V A 603
4AC4SOFTWAREARG A:33 , PRO A:35 , LEU A:36 , TRP A:37 , HIS A:475 , MPD A:606 , HOH A:755BINDING SITE FOR RESIDUE SO4 A 604
5AC5SOFTWAREGLU A:283 , THR A:284 , GLY A:286 , TRP A:402 , HOH A:944BINDING SITE FOR RESIDUE MPD A 605
6AC6SOFTWAREARG A:33 , TRP A:37 , GLY A:484 , VAL A:485 , ASN A:506 , VAL A:513 , SO4 A:604BINDING SITE FOR RESIDUE MPD A 606
7AC7SOFTWARELEU A:408 , PHE A:409 , LYS A:455 , HOH A:710 , HOH A:834BINDING SITE FOR RESIDUE MPD A 607

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4RYX)

(-) 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:510
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhh........ee.eeee.......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.hhhhhhhhh....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
                 4ryx A   4 QVEHPAGGYKKLFETVEELSSPLTAHVTGRIPLWLTGSLLRCGPGLFEVGSEPFYHLFDGQALLHKFDFKEGHVTYHRRFIRTDAYVRAMTEKRIVITEFGTCAFPDFRGVEVTDNALVNIYPVGEDYYACTETNFITKVNPETLETIKQVDLCNYVSVNGATAHPHIENDGTVYNIGNCFGSIAYNIVKIPPLQADKEDPISKSEIVVQFPCSDRFKPSYVHSFGLTPNYIVFVETPVKINLFKFLSGANYMDCFESNETMGVWLHIADKKRKKYINNKYRTSPFNLFHHINTYEDHEFLIVDLCCWKGFEFVYNYLYLANLRENWEEVKKNARKAPQPEVRRYVLPLNIDKADTGKNLVTLPNTTATAILCSDETIWLEPEVLFSGPRQAFEFPQINYQKYGGKPYTYAYGLGLNHFVPDRLCKLNVKTKETWVWQEPDSYPSEPIFVSHPDALEEDDGVVLSVVVSPGAGQKPAYLLILNAKDLSEVARAEVEINIPVTFHGLFKKS 533
                                    13        23        33        43        53        63        73        83        93       103      |125       135       145       155       165       175       185       195 ||    208       218       228       238       248       258       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533
                                                                                                                                    110|                                                                       197|                                                              266|                                                                                                                                                                                                                                                                     
                                                                                                                                     123                                                                        201                                                               272
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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 4RYX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (20, 20)

Asymmetric Unit(hide GO term definitions)

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  RPE65_BOVIN | Q28175
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  3.1.1.64
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        RPE65_BOVIN | Q28175: 3fsn 3kvc 4f2z 4f30 4f3a 4f3d 4rsc 4rse 4ryy 4ryz 4zhk 5ul5 5ulg

(-) Related Entries Specified in the PDB File

3fsn 4rsc 4ryy 4ryz