2O52

Crystal structure of human RAB4B in complex with GDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of human RAB4B in complex with GDP

Zhu, H.Tempel, W.Wang, J.Shen, Y.Landry, R.Arrowsmith, C.H.Edwards, A.M.Sundstrom, M.Weigelt, J.Bochkarev, A.Park, H.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ras-related protein Rab-4B
A, B
200Homo sapiensMutation(s): 0 
Gene Names: RAB4B
Find proteins for P61018 (Homo sapiens)
Go to Gene View: RAB4B
Go to UniProtKB:  P61018
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

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

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Download CCD File 
A
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
BME
Query on BME

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Download CCD File 
A, B
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.213 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 67.528α = 90.00
b = 67.528β = 90.00
c = 179.955γ = 90.00
Software Package:
Software NamePurpose
ARP/wARPmodel building
MolProbitymodel building
SCALEPACKdata scaling
REFMACrefinement
PHASERphasing
Cootmodel building
PDB_EXTRACTdata extraction
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-12-19
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description