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(-) Description

Title :  CRYSTAL STRUCTURE OF RPE65 IN COMPLEX WITH S-EMIXUSTAT AND PALMITATE
 
Authors :  P. D. Kiser, K. Palczewski
Date :  17 Dec 14  (Deposition) - 27 May 15  (Release) - 27 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  7-Bladed Beta Propeller, Monotopic Membrane Protein, Non-Heme Iron Enzyme, Retinoid Isomerase, Isomerase (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, B
    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

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
1A5V2Ligand/Ion(1S)-3-AMINO-1-[3-(CYCLOHEXYLMETHOXY)PHENYL]PROPAN-1-OL
2ACE2Mod. Amino AcidACETYL GROUP
3FE22Ligand/IonFE (II) ION
4PLM2Ligand/IonPALMITIC ACID

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:180 , HIS A:241 , HIS A:313 , HIS A:527 , PLM A:602BINDING SITE FOR RESIDUE FE2 A 601
2AC2SOFTWARELEU A:60 , VAL A:134 , HIS A:180 , HIS A:241 , PHE A:312 , HIS A:313 , TYR A:338 , GLU A:417 , PHE A:418 , LEU A:439 , PHE A:442 , VAL A:524 , HIS A:527 , FE2 A:601 , A5V A:603BINDING SITE FOR RESIDUE PLM A 602
3AC3SOFTWAREPHE A:61 , PHE A:103 , VAL A:134 , THR A:147 , GLU A:148 , ASN A:194 , TYR A:239 , ILE A:259 , TYR A:275 , TYR A:338 , PLM A:602BINDING SITE FOR RESIDUE A5V A 603
4AC4SOFTWAREHIS B:180 , HIS B:241 , HIS B:313 , HIS B:527 , PLM B:602BINDING SITE FOR RESIDUE FE2 B 601
5AC5SOFTWARELEU B:60 , VAL B:134 , 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 , A5V B:603BINDING SITE FOR RESIDUE PLM B 602
6AC6SOFTWAREPHE B:61 , PHE B:103 , VAL B:134 , THR B:147 , GLU B:148 , ASN B:194 , TYR B:239 , TYR B:275 , TYR B:338 , PLM B:602 , HOH B:724BINDING SITE FOR RESIDUE A5V B 603

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4RYZ)

(-) 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........ee.eeee.......eeeeeeeeee.ee..ee.......eeeeeeeeee..eeeeeeee..hhhhhhhhhhh.....................eeeee..eeeee....eeeee......eeeeee.hhh..........ee.....eeeeeee..eeeeeee........hhhhhheeeeee..............ee...eeeeee..eeehhhhhhhhhhhhh..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
                 4ryz A   1 xSSQVEHPAGGYKKLFETVEELSSPLTAHVTGRIPLWLTGSLLRCGPGLFEVGSEPFYHLFDGQALLHKFDFKEGHVTYHRRFIRTDAYVRAMTEKRIVITEFGTCAFPEVTDNALVNIYPVGEDYYACTETNFITKVNPETLETIKQVDLCNYVSVNGATAHPHIENDGTVYNIGNCFIAYNIVKIPPLQADKEDPISKSEIVVQFPCSDRFKPSYVHSFGLTPNYIVFVETPVKINLFKFLSSWSLWGANYMDCFESNETMGVWLHIADKKRKKYINNKYRTSPFNLFHHINTYEDHEFLIVDLCCWKGFEFVYNYLYLANLRENWEEVKKNARKAPQPEVRRYVLPLNIDKADTGKNLVTLPNTTATAILCSDETIWLEPEVLFSGPRQAFEFPQINYQKYGGKPYTYAYGLGLNHFVPDRLCKLNVKTKETWVWQEPDSYPSEPIFVSHPDALEEDDGVVLSVVVSPGAGQKPAYLLILNAKDLSEVARAEVEINIPVTFHGLFKKS 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 
                            |                                                                                                         109|                                                                  196|                                                                                                                                                                                                                                                                                                                                           
                            1-ACE                                                                                                      127                                                                   202                                                                                                                                                                                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:511
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               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..eeehhhhhhhhhhhhh..hhh.eee.....eeeeeee....ee...eeee..eeeeeeeeeeee..eeeeeeeeee...hhhhhhhhhhhh.hhhhhhhhhh...eeeeeeeeee...hhhhh............eeee....eeeee.eeee....eeeeeee.hhhhhh.....eeeeeeee..eeeeeeeee.....eeee..........eeee.........eeeeeeee........eeeeeee.....eeeeeee.........eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ryz B   1 xSSQVEHPAGGYKKLFETVEELSSPLTAHVTGRIPLWLTGSLLRCGPGLFEVGSEPFYHLFDGQALLHKFDFKEGHVTYHRRFIRTDAYVRAMTEKRIVITEFGTCAFPEVTDNALVNIYPVGEDYYACTETNFITKVNPETLETIKQVDLCNYVSVNGATAHPHIENDGTVYNIGNCFIAYNIVKIPPLQADKEDPISKSEIVVQFPCSDRFKPSYVHSFGLTPNYIVFVETPVKINLFKFLSSWSLWGANYMDCFESNETMGVWLHIADKKRKKYINNKYRTSPFNLFHHINTYEDHEFLIVDLCCWKGFEFVYNYLYLANLRENWEEVKKNARKAPQPEVRRYVLPLNIDKADTGKNLVTLPNTTATAILCSDETIWLEPEVLFSGPRQAFEFPQINYQKYGGKPYTYAYGLGLNHFVPDRLCKLNVKTKETWVWQEPDSYPSEPIFVSHPDALEEDDGVVLSVVVSPGAGQKPAYLLILNAKDLSEVARAEVEINIPVTFHGLFKKS 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 
                            1-ACE                                                                                                     109|                                                                  196|                                                                                                                                                                                                                                                                                                                                           
                                                                                                                                       127                                                                   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 4RYZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (20, 20)

Asymmetric/Biological Unit(hide GO term definitions)

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  4ryz
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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 4ryx 4ryy 4zhk 5ul5 5ulg

(-) Related Entries Specified in the PDB File

3fsn 4rsc 4ryx 4ryy