5DGY Signaling Protein date Aug 28, 2015
title Crystal Structure Of Rhodopsin Bound To Visual Arrestin
authors X.E.Zhou, X.Gao, Y.Kang, Y.He, P.W.De Waal, K.M.Suino-Powell, M.Wa K.Melcher, H.E.Xu
compound source
Molecule: Endolysin,Rhodopsin,S-Arrestin
Chain: A, B, C, D
Synonym: Lysis Protein,Lysozyme,Muramidase,Opsin-2,48 Kda P Retinal S-Antigen,S-Ag,Rod Photoreceptor Arrestin;
Engineered: Yes
Mutation: Yes
Organism_scientific: Enterobacteria Phage T4, Homo Sapiens, Musculus;
Organism_common: Human, Mouse
Organism_taxid: 10665, 9606, 10090
Gene: Rho, Opn2, Sag
Expression_system: Homo Sapiens
Expression_system_taxid: 9606
Expression_system_cell_line: Hek293s
symmetry Space Group: P 21 21 21
R_factor 0.285 R_Free 0.335
length a length b length c angle alpha angle beta angle gamma
107.484 107.258 460.314 90.00 90.00 90.00
method X-Ray Diffractionresolution 7.70 Å
enzyme Hydrolase E.C. BRENDA
A, D, C, B

Primary referenceX-ray laser diffraction for structure determination of the rhodopsin-arrestin complex., Zhou XE, Gao X, Barty A, Kang Y, He Y, Liu W, Ishchenko A, White TA, Yefanov O, Han GW, Xu Q, de Waal PW, Suino-Powell KM, Boutet S, Williams GJ, Wang M, Li D, Caffrey M, Chapman HN, Spence JC, Fromme P, Weierstall U, Stevens RC, Cherezov V, Melcher K, Xu HE, Sci Data. 2016 Apr 12;3:160021. doi: 10.1038/sdata.2016.21. PMID:27070998
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1111 Kb) [Save to disk]
  • Biological Unit Coordinates (5dgy.pdb1.gz) 574 Kb
  • Biological Unit Coordinates (5dgy.pdb2.gz) 533 Kb
  • CSU: Contacts of Structural Units for 5DGY
  • Structure Factors (110 Kb)
  • Retrieve 5DGY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5DGY from S2C, [Save to disk]
  • Re-refined 5dgy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5DGY in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 5DGY
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5dgy from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5dgy_A] [5dgy] [5dgy_D] [5dgy_B] [5dgy_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5DGY: [Arrestin_C ] by SMART
  • Other resources with information on 5DGY
  • Community annotation for 5DGY at PDBWiki (http://pdbwiki.org)

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