3Q5D

crystal structure of human Atlastin-1 (residues 1-447) bound to GDP, crystal form 1

Structural Biology Knowledgebase: 3Q5D SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.250
  • R-Value Work: 0.188

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3Q5D

Classification: HYDROLASE

Total Structure Weight: 52255.11

Macromolecule Entities
Molecule Chains Length Organism Details
Atlastin-1 A 447 Homo sapiens EC#: 3.6.5 IUBMB
Fragment: G and middle domain, UNP residues 1-447
Gene Name(s): ATL1 Gene View GBP3 Gene View SPG3A

Small Molecules
Ligands 2 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
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.250
  • R-Value Work: 0.188
  • Space Group: P 65 2 2

Unit Cell:

Length (Å) Angle (°)
a = 145.35 α = 90.00
b = 145.35 β = 90.00
c = 104.17 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-12-28
  • Released Date: 2011-01-19
  • Deposition author(s): Byrnes, L.J., Sondermann, H.

Revision History

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