SMTL ID : 3it8.1 (1 other biounit)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-3-3-mer

Ligands

9 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 5 residues within 4Å: Chain D: K.4, N.6, T.8, Y.22, I.94 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:I.94 Hydrogen bonds: D:N.6, D:T.8, D:Y.22 Water bridges: D:K.4 NAG.2: 3 residues within 4Å: Chain D: N.52, S.54, R.55 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:R.55 Hydrogen bonds: D:N.52 NAG.3: 2 residues within 4Å: Chain D: N.83, S.85 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.85 NAG.4: 6 residues within 4Å: Chain E: K.4, N.6, T.8, Y.22, I.94, E.111 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:I.94 Hydrogen bonds: E:N.6, E:Y.22, E:Y.22, E:E.111 Water bridges: E:K.4 NAG.5: 3 residues within 4Å: Chain E: N.52, S.54, R.55 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:R.55 Hydrogen bonds: E:N.52 NAG.6: 2 residues within 4Å: Chain E: N.83, S.85 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:S.85 NAG.7: 6 residues within 4Å: Chain F: K.4, N.6, T.8, Y.22, I.94, E.111 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:I.94 Hydrogen bonds: F:N.6, F:T.8, F:E.111 Water bridges: F:K.4 NAG.8: 3 residues within 4Å: Chain F: N.52, S.54, R.55 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:R.55 Hydrogen bonds: F:N.52 NAG.9: 2 residues within 4Å: Chain F: N.83, S.85 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:S.85

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, Z. et al., Crystal structure of TNFalpha complexed with a poxvirus MHC-related TNF binding protein. Nat.Struct.Mol.Biol. (2009)

Release Date

2009-10-20

Peptides

Tumor necrosis factor: ABC
2L protein: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Tumor necrosis factor

2L protein

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