6IYB Transport Protein date Dec 14, 2018
title Structure Of Human Orp1 Ank - Rab7 Complex
authors J.Tong, Y.J.Im
compound source
Molecule: Ras-Related Protein Rab-7a
Chain: A, C
Fragment: Unp Residues 2-195
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rab7a
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)

Molecule: Oxysterol-Binding Protein-Related Protein 1
Chain: B, D
Fragment: Unp Residues 5-152
Synonym: Osbp-Related Protein 1
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Osbpl1a
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Phis2-Thr
symmetry Space Group: P 21 21 21
R_factor 0.195 R_Free 0.232
crystal
cell
length a length b length c angle alpha angle beta angle gamma
55.136 117.222 130.476 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.09 Å
ligand GTP, MG enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, C


Primary referenceStructural basis of human ORP1-Rab7 interaction for the late-endosome and lysosome targeting., Tong J, Tan L, Chun C, Im YJ, PLoS One. 2019 Feb 5;14(2):e0211724. doi: 10.1371/journal.pone.0211724., eCollection 2019. PMID:30721249
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (112 Kb) [Save to disk]
  • Biological Unit Coordinates (6iyb.pdb1.gz) 55 Kb
  • Biological Unit Coordinates (6iyb.pdb2.gz) 54 Kb
  • LPC: Ligand-Protein Contacts for 6IYB
  • CSU: Contacts of Structural Units for 6IYB
  • Structure Factors (479 Kb)
  • Retrieve 6IYB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6IYB from S2C, [Save to disk]
  • View 6IYB 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 6IYB
  • 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 6iyb from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6iyb_C] [6iyb_B] [6iyb_D] [6iyb_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6IYB
  • Community annotation for 6IYB at PDBWiki (http://pdbwiki.org)

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