1N6I

Crystal Structure of Human Rab5a A30P mutant Complex with GDP

Structural Biology Knowledgebase: 1N6I SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.214
  • R-Value Work: 0.178

Literature

Macromolecules
Sequence Display for 1N6I

Classification: Protein Transport

Total Structure Weight: 19559.40

Macromolecule Entities
Molecule Chains Length Organism Details
Ras-related protein Rab-5A A 170 Homo sapiens Fragment: GTPASE DOMAIN
Mutation: A30P
Gene Name(s): RAB5A Gene View RAB5
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BME
Query on BME

A BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.214
  • R-Value Work: 0.178
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 35.86 α = 90.00
b = 63.91 β = 90.00
c = 66.06 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-11-11
  • Released Date: 2002-11-27
  • Deposition author(s): Zhu, G., Liu, J., Terzyan, S., Zhai, P., Li, G., Zhang, X.C.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4