› 2az5

X-ray diffraction
2.1Å resolution

Crystal Structure of TNF-alpha with a small molecule inhibitor

Released:
DOI: 10.2210/pdb2az5/pdb
PDB entry 2az5 coloured by chain, front view.
PDB entry 2az5 coloured by chain, side view.
PDB entry 2az5 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Small-molecule inhibition of TNF-alpha.
He MM, Smith AS, Oslob JD, Flanagan WM, Braisted AC, Whitty A, Cancilla MT, Wang J, Lugovskoy AA, Yoburn JC, Fung AD, Farrington G, Eldredge JK, Day ES, Cruz LA, Cachero TG, Miller SK, Friedman JE, Choong IC, Cunningham BC
Science 310 1022-5 (2005)
PMID: 16284179

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-134293 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Tumor necrosis factor, soluble form Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 148 amino acids
Theoretical weight: 16.41 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P01375 (Residues: 86-233; Coverage: 64%)
Gene names: TNF, TNFA, TNFSF2
Sequence domains: TNF(Tumour Necrosis Factor) family
Structure domains: Jelly Rolls

Ligands and Environments

1 bound ligand:
Ligand 307 2 x 307
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL7-1
Spacegroup: R3
Unit cell:
a: 165.254Å b: 165.254Å c: 63.728Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.227 0.22 0.278
Expression system: Escherichia coli BL21(DE3)

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Citations

47 review citations

Reaching for high-hanging fruit in drug discovery at protein-protein interfaces.
Wells et al. (2007)
46 more

191 mentions without citation

In silico structure-based approaches to discover protein-protein interaction-targeting drugs.
Shin et al. (2017)
190 more