4IDN

Human atlastin-1 1-446, C-his6, GppNHp

Structural Biology Knowledgebase: 4IDN SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.218
  • R-Value Work: 0.173

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4IDN

Classification: HYDROLASE

Total Structure Weight: 106096.91

Macromolecule Entities
Molecule Chains Length Organism Details
Atlastin-1 A, B 457 Homo sapiens EC#: 3.6.5 IUBMB
Fragment: cytoplasmic domain (UNP residues 1-446)
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
GNP
Query on GNP

A, B PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
GNP N/A in BindingDB
Kd: 5770 nM  BindingMOAD
Kd: 5770 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.218
  • R-Value Work: 0.173
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 49.69 α = 90.00
b = 115.78 β = 90.00
c = 181.13 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-12-12
  • Released Date: 2013-01-09
  • Deposition author(s): Byrnes, L.J., Singh, A., Szeto, K., Benvin, N.M., O'Donnell, J.P., Zipfel, W.R., Sondermann, H.

Revision History

  • 2013-02-20
    Type: Citation | Details: Citation update
  • 2013-02-06
    Type: Citation | Details: Citation update