2HEI

Crystal structure of human RAB5B in complex with GDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.262 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of human RAB5B in complex with GDP

Hong, B.Shen, L.Wang, J.Tempel, W.Landry, R.Arrowsmith, C.H.Edwards, A.M.Sundstrom, M.Weigelt, J.Bochkarev, A.Park, H.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ras-related protein Rab-5B AB179Homo sapiensMutation(s): 0 
Gene Names: RAB5B
Find proteins for P61020 (Homo sapiens)
Explore P61020 
Go to UniProtKB:  P61020
NIH Common Fund Data Resources
PHAROS:  P61020
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download Ideal Coordinates CCD File 
A, B
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
D1D
Query on D1D

Download Ideal Coordinates CCD File 
A, B
(4S,5S)-1,2-DITHIANE-4,5-DIOL
C4 H8 O2 S2
YPGMOWHXEQDBBV-QWWZWVQMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.262 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.302α = 90
b = 78.37β = 90
c = 95.501γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ARP/wARPmodel building
MolProbitymodel building

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-07-04
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description