2HEI

Crystal structure of human RAB5B in complex with GDP

• PDB DOI: https://doi.org/10.2210/pdb2HEI/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-06-21 Released: 2006-07-04 
• Deposition Author(s): Hong, B., Shen, L., Wang, J., Tempel, W., Landry, R., Arrowsmith, C.H., Edwards, A.M., Sundstrom, M., Weigelt, J., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

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

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 40.74 kDa 
• Atom Count: 2,764 
• Modelled Residue Count: 328 
• Deposited Residue Count: 358 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related protein Rab-5B	A, B	179	Homo sapiens	Mutation(s): 0  Gene Names: RAB5B EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P61020 (Homo sapiens) Explore P61020  Go to UniProtKB:  P61020
PHAROS:  P61020 GTEx:  ENSG00000111540

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	C [auth A], E [auth B]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
D1D	D [auth A], F [auth B]	(4S,5S)-1,2-DITHIANE-4,5-DIOL C4 H8 O2 S2 YPGMOWHXEQDBBV-QWWZWVQMSA-N

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 = 41.302	α = 90
b = 78.37	β = 90
c = 95.501	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ARP/wARP	model building
MolProbity	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-07-04 
Deposition Author(s): Hong, B., Shen, L., Wang, J., Tempel, W., Landry, R., Arrowsmith, C.H., Edwards, A.M., Sundstrom, M., Weigelt, J., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

Revision History  

• 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
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description