3VD8

Crystal structure of human AIM2 PYD domain with MBP fusion

Structural Biology Knowledgebase: 3VD8 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.221
  • R-Value Work: 0.182

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3VD8

Classification: SUGAR BINDING PROTEIN SIGNALING PROTEIN

Total Structure Weight: 55045.25

Macromolecule Entities
Molecule Chains Length Organism Details
Maltose-binding periplasmic protein, Interferon-inducible protein AIM2 A 489 Escherichia coli Homo sapiens Fragment: PYD domain (UNP Residues 1-107)
Mutation: D82A, K83A, E172A, N173A, K239A
Gene Name(s): AIM2 Gene View malE Z5632 ECs5017

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
MTT
Query on MTT

A MALTOTETRAOSE
C24 H42 O21
LUEWUZLMQUOBSB-ZLBHSGTGSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
K
Query on K

A POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.221
  • R-Value Work: 0.182
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 61.60 α = 90.00
b = 91.93 β = 90.00
c = 100.28 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-01-04
  • Released Date: 2013-01-16
  • Deposition author(s): Jin, T.C., Perry, A., Smith, P., Xiao, T.S.

Revision History

  • 2013-06-05
    Type: Citation | Details: Citation update
  • 2013-02-13
    Type: Entry authorship | Details: Update entry authorship
  • 2013-02-13
    Type: Citation | Details: Update citation authorship