3IT8

Crystal structure of TNF alpha complexed with a poxvirus MHC-related TNF binding protein

Structural Biology Knowledgebase: 3IT8 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.266
  • R-Value Work: 0.236

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3IT8

Classification: IMMUNE SYSTEM

Total Structure Weight: 335670.53

Macromolecule Entities
Molecule Chains Length Organism Details
Tumor necrosis factor A, B, C..., G, H, IA, B, C, G, H, I 161 Homo sapiens Fragment: Tumor necrosis factor, soluble form, UNP residues 82-233
Mutation: D143L
Gene Name(s): TNF Gene View TNFA TNFSF2
2L protein D, E, F..., J, K, LD, E, F, J, K, L 324 Tanapox virus Gene Name(s): 2L

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NAG
Query on NAG

D, E, F, J, K, L N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.266
  • R-Value Work: 0.236
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 101.66 α = 90.00
b = 170.29 β = 92.04
c = 122.00 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-08-27
  • Released Date: 2009-10-20
  • Deposition author(s): Yang, Z., West Jr., A.P., Bjorkman, P.J.

Revision History

  • 2015-12-09
    Type: Citation | Details: Citation update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update