3L43

Crystal structure of the dynamin 3 GTPase domain bound with GDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of the dynamin 3 GTPase domain bound with GDP

Yang, S.Tempel, W.Tong, Y.Nedyalkova, L.Guan, X.Crombet, L.Arrowsmith, C.H.Edwards, A.M.Bountra, C.Weigelt, J.Bochkarev, A.Park, H.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dynamin-3
A, B, C, D
319Homo sapiensMutation(s): 1 
Gene Names: DNM3 (KIAA0820)
EC: 3.6.5.5
Find proteins for Q9UQ16 (Homo sapiens)
Go to Gene View: DNM3
Go to UniProtKB:  Q9UQ16
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

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

Download SDF File 
Download CCD File 
A, B, C, D
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.229 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 49.286α = 90.00
b = 166.500β = 109.02
c = 74.985γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
BUSTERrefinement
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
PHASERphasing
HKL-2000data scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-01-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2014-06-11
    Type: Refinement description
  • Version 1.3: 2017-11-01
    Type: Refinement description