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(-) Description

Title :  CRYSTAL STRUCTURE OF RPE65 IN COMPLEX WITH MB-004 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 :  2.20
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
18D72Ligand/Ion(1R)-3-AMINO-1-{3-[(2-PROPYLPENTYL)OXY]PHENYL}PROPAN-1-OL
2FE22Ligand/IonFE (II) ION
3NA2Ligand/IonSODIUM ION
4PG62Ligand/Ion1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE
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 , LEU A:437 , PHE A:442 , PRO A:444 , VAL A:524 , HIS A:527 , FE2 A:601 , 8D7 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:175 , GLY A:176 , HIS A:241 , PHE A:279 , TYR A:338 , PLM A:602binding site for residue 8D7 A 603
04AC4SOFTWAREGLN A:461 , PG6 A:605binding site for residue NA A 604
05AC5SOFTWAREGLN A:4 , VAL A:459 , TRP A:460 , GLN A:461 , GLU A:462 , PRO A:463 , NA A:604binding site for residue PG6 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 , LEU B:437 , PHE B:442 , PRO B:444 , VAL B:524 , HIS B:527 , FE2 B:601 , 8D7 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:175 , GLY B:176 , PHE B:264 , PHE B:279 , PLM B:602binding site for residue 8D7 B 603
09AC9SOFTWAREGLN B:4 , VAL B:459 , TRP B:460 , GLN B:461 , PRO B:463 , NA B:605 , HOH B:885binding site for residue PG6 B 604
10AD1SOFTWAREGLN B:461 , PG6 B:604 , HOH B:885binding site for residue NA B 605

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5UL5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5UL5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5UL5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5UL5)

(-) Exons   (0, 0)

(no "Exon" information available for 5UL5)

(-) 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:511
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhh........eeeeeee.......eeeeeeee...ee..ee........eeeeeeeee..eeeeeeee..hhhhhhhhhhh.....................eeeee..eeeee....eeeee......eeeeee.hhh..........ee.....eeeeeee..eeeeeee........hhhhhheeeeee..............ee...eeeeee..eeehhhhhh.hhhhhh..hhh.eee.....eeeeeee....eeeeeeeee..eeeeeeeeeeee..eeeeeeeeee...hhhhhhhhhhhh.hhhhhhhhhh...eeeeeeeeee...hhhhh............eeee....eeeee.eeeee...eeeeeee.hhhhhh.....eeeeeeee..eeeeeeeee.....eeee..........eeee.........eeeeeeee........eeeeeee.....eeeeeee........eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ul5 A   1 MSSQVEHPAGGYKKLFETVEELSSPLTAHVTGRIPLWLTGSLLRCGPGLFEVGSEPFYHLFDGQALLHKFDFKEGHVTYHRRFIRTDAYVRAMTEKRIVITEFGTCAFVEVTDNALVNIYPVGEDYYACTETNFITKVNPETLETIKQVDLCNYVSVNGATAHPHIENDGTVYNIGNCFIAYNIVKIPPLQADKEDPISKSEIVVQFPCSDRFKPSYVHSFGLTPNYIVFVETPVKINLFKFLSSWSLWGANYMDCFESNETMGVWLHIADKKRKKYINNKYRTSPFNLFHHINTYEDHEFLIVDLCCWKGFEFVYNYLYLANLRENWEEVKKNARKAPQPEVRRYVLPLNIDKADTGKNLVTLPNTTATAILCSDETIWLEPEVLFSGPRQAFEFPQINYQKYGGKPYTYAYGLGLNHFVPDRLCKLNVKTKETWVWQEPDSYPSEPIFVSHPDALEEDDGVVLSVVVSPGAGQKPAYLLILNAKDLSEVARAEVEINIPVTFHGLFKKS 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       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532 
                                                                                                                                     108|                                                                   196|                                                                                                                                                                                                                                                                                                                                           
                                                                                                                                      126                                                                    202                                                                                                                                                                                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:513
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhh........eeeeeee.......eeeeeeee...ee..ee........eeeeeeeee..eeeeeeee..hhhhhhhhhhh.......................eeeee..eeeee....eeeee......eeeeee.hhh..........ee.....eeeeeee..eeeeeee........hhhhhheeeeeee.............ee...eeeeee..eeehhhhhh.hhhhhh..hhh.eee.....eeeeeee....eeeeeeeee..eeeeeeeeeeee..eeeeeeeeee...hhhhhhhhhhhh.hhhhhhhhhh...eeeeeeeeee...hhhhh............eeee....eeeee.eeeee...eeeeeee.hhhhhh.....eeeeeeee..eeeeeeeee.....eeee..........eeee.........eeeeeeee........eeeeeee.....eeeeeee........eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ul5 B   1 MSSQVEHPAGGYKKLFETVEELSSPLTAHVTGRIPLWLTGSLLRCGPGLFEVGSEPFYHLFDGQALLHKFDFKEGHVTYHRRFIRTDAYVRAMTEKRIVITEFGTCAFPGVEVTDNALVNIYPVGEDYYACTETNFITKVNPETLETIKQVDLCNYVSVNGATAHPHIENDGTVYNIGNCFIAYNIVKIPPLQADKEDPISKSEIVVQFPCSDRFKPSYVHSFGLTPNYIVFVETPVKINLFKFLSSWSLWGANYMDCFESNETMGVWLHIADKKRKKYINNKYRTSPFNLFHHINTYEDHEFLIVDLCCWKGFEFVYNYLYLANLRENWEEVKKNARKAPQPEVRRYVLPLNIDKADTGKNLVTLPNTTATAILCSDETIWLEPEVLFSGPRQAFEFPQINYQKYGGKPYTYAYGLGLNHFVPDRLCKLNVKTKETWVWQEPDSYPSEPIFVSHPDALEEDDGVVLSVVVSPGAGQKPAYLLILNAKDLSEVARAEVEINIPVTFHGLFKKS 533
                                    10        20        30        40        50        60        70        80        90       100       125       135       145       155       165       175       185       195||     210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530   
                                                                                                                                      109|                                                                    196|                                                                                                                                                                                                                                                                                                                                           
                                                                                                                                       125                                                                     202
   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 5UL5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5UL5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5UL5)

(-) Gene Ontology  (20, 20)

Asymmetric/Biological Unit(hide GO term definitions)

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  RPE65_BOVIN | Q28175
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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 4ryx 4ryy 4ryz 4zhk 5ulg

(-) Related Entries Specified in the PDB File

5ulg