6IYB

Structure of human ORP1 ANK - Rab7 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.091 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural basis of human ORP1-Rab7 interaction for the late-endosome and lysosome targeting.

Tong, J.Tan, L.Chun, C.Im, Y.J.

(2019) PLoS ONE 14: e0211724-e0211724


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ras-related protein Rab-7a
A, C
199Homo sapiensMutation(s): 1 
Gene Names: RAB7A (RAB7)
Find proteins for P51149 (Homo sapiens)
Go to Gene View: RAB7A
Go to UniProtKB:  P51149
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Oxysterol-binding protein-related protein 1
B, D
154Homo sapiensMutation(s): 0 
Gene Names: OSBPL1A (ORP1, OSBP8, OSBPL1, OSBPL1B)
Find proteins for Q9BXW6 (Homo sapiens)
Go to Gene View: OSBPL1A
Go to UniProtKB:  Q9BXW6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download SDF File 
Download CCD File 
A, C
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.091 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 55.136α = 90.00
b = 117.222β = 90.00
c = 130.476γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-12-14 
  • Released Date: 2019-03-13 
  • Deposition Author(s): Tong, J., Im, Y.J.

Funding OrganizationLocationGrant Number
National Research Foundation (Korea)Korea, Republic OfNRF-2017R1A2B4004914

Revision History 

  • Version 1.0: 2019-03-13
    Type: Initial release