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(-) Description

Title :  CRYSTAL STRUCTURE OF RPE65 IN COMPLEX WITH MB-002
 
Authors :  P. D. Kiser, K. Palczewski
Date :  25 Apr 15  (Deposition) - 27 May 15  (Release) - 27 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.09
Chains :  Asym./Biol. Unit :  A,B
Keywords :  7-Bladed Beta Propeller, Monotopic Membrane Protein, Non-Heme Iron Protein, Retinoid Isomerase, Smooth Endoplasmic Reticulum, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. D. Kiser, K. Palczewski
Crystal Structure Of Rpe65 In Complex With Mb-002
To Be Published
PubMed: search

(-) 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
    Tissue: RETINAL PIGMENT EPITHELIUM

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 15)

Asymmetric/Biological Unit (7, 15)
No.NameCountTypeFull Name
1A8V2Ligand/Ion(1S)-1-[3-(CYCLOHEXYLMETHOXY)PHENYL]PROPANE-1,3-DIOL
2A9V2Ligand/Ion(1R)-1-[3-(CYCLOHEXYLMETHOXY)PHENYL]PROPANE-1,3-DIOL
3ACE2Mod. Amino AcidACETYL GROUP
4FE22Ligand/IonFE (II) ION
5NA2Ligand/IonSODIUM ION
6PG42Ligand/IonTETRAETHYLENE GLYCOL
7PGE3Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:180 , HIS A:241 , HIS A:313 , HIS A:527 , A9V A:607binding site for residue FE2 A 601
02AC2SOFTWAREGLN A:4 , VAL A:459 , TRP A:460 , GLN A:461 , PRO A:463 , NA A:603binding site for residue PG4 A 602
03AC3SOFTWAREGLN A:461 , PG4 A:602 , HOH A:940binding site for residue NA A 603
04AC4SOFTWAREASP A:320 , TYR A:431 , THR A:432 , LYS A:453binding site for residue PGE A 604
05AC5SOFTWAREGLY A:484 , ASN A:506 , HOH A:807binding site for residue PGE A 605
06AC6SOFTWAREPHE A:61 , PHE A:103 , VAL A:134 , THR A:147 , GLU A:148 , ASN A:175 , ASN A:194 , TYR A:239 , HIS A:241 , TYR A:275 , TYR A:338binding site for residue A8V A 606
07AC7SOFTWARELEU A:60 , HIS A:241 , PHE A:312 , TYR A:338 , GLU A:417 , PHE A:418 , PHE A:442 , VAL A:524 , HIS A:527 , FE2 A:601binding site for residue A9V A 607
08AC8SOFTWAREHIS B:180 , HIS B:241 , HIS B:313 , HIS B:527 , A9V B:606binding site for residue FE2 B 601
09AC9SOFTWAREGLN B:4 , VAL B:459 , TRP B:460 , GLN B:461 , PRO B:463 , NA B:603binding site for residue PG4 B 602
10AD1SOFTWAREGLN B:461 , PG4 B:602 , HOH B:958binding site for residue NA B 603
11AD2SOFTWARETYR B:318 , ASP B:320 , PRO B:430 , TYR B:431 , LYS B:453 , HOH B:702binding site for residue PGE B 604
12AD3SOFTWAREPHE B:61 , PHE B:103 , VAL B:134 , THR B:147 , GLU B:148 , ASN B:175 , ASN B:194 , TYR B:239 , HIS B:241 , TYR B:275 , TYR B:338binding site for residue A8V B 605
13AD4SOFTWARELEU B:60 , PHE B:61 , HIS B:241 , HIS B:313 , TYR B:338 , GLU B:417 , PHE B:418 , PHE B:442 , VAL B:524 , HIS B:527 , FE2 B:601binding site for residue A9V B 606

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ZHK)

(-) 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........hhhhhheeeeeee.............ee...eeeeee..eeehhhhhh.hhhhhh..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
                 4zhk 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........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.eeee....eeeeeee.hhhhhh.....eeeeeeee..eeeeeeeee.....eeee..........eeee.........eeeeeeee........eeeeeee.....eeeeeee........eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zhk 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 4ZHK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

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

(-) Related Entries Specified in the PDB File

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