1YHN

Structure basis of RILP recruitment by Rab7

Structural Biology Knowledgebase: 1YHN SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.278
  • R-Value Work: 0.268

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1YHN

Classification: Protein transport

Total Structure Weight: 31835.76

Macromolecule Entities
Molecule Chains Length Organism Details
Ras-related protein Rab-7 A 207 Homo sapiens Mutation: Q67L
Gene Name(s): RAB7A Gene View RAB7
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Rab interacting lysosomal protein B 65 Homo sapiens Fragment: RILP effector domain
Gene Name(s): RILP Gene View PP10141
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
GTP
Query on GTP

A GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.278
  • R-Value Work: 0.268
  • Space Group: P 65 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 93.13 α = 90.00
b = 93.13 β = 90.00
c = 132.83 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-01-10
  • Released Date: 2005-05-17
  • Deposition author(s): Wu, M., Wang, T., Hong, W., Song, H.

Revision History

  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4