SMTL ID : 7kpa.1

asymmetric hTNF-alpha

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-trimer

Ligands

1 x D84: 5-(1-{[2-(difluoromethoxy)phenyl]methyl}-2-{[3-(2-oxopyrrolidin-1-yl)phenoxy]methyl}-1H-benzimidazol-6-yl)pyridin-2(1H)-one(Non-covalent)

D84.1: 27 residues within 4Å: Chain A: K.12, L.58, Y.60, S.61, Y.120, L.121, G.122, G.123, V.124, Y.152, I.156, L.158 Chain B: L.58, Y.60, Y.120, G.122, G.123, I.156 Chain C: L.58, Y.60, S.61, Q.62, Y.120, L.121, G.122, G.123, Y.152 17 PLIP interactions: 9 interactions with chain A, 6 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: A:L.58, A:Y.120, A:Y.120, A:V.124, A:I.156, C:L.58, C:Y.60, C:Y.120, C:Y.152, B:Y.120 Hydrogen bonds: A:S.61, A:L.121, B:Y.120 Water bridges: A:L.158, A:L.158 pi-Stacking: C:Y.60, C:Y.120

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lightwood, D.J. et al., A conformation-selective monoclonal antibody against a small molecule-stabilised signalling-deficient form of TNF. Nat Commun (2021)

Release Date

2021-01-13

Peptides

Tumor necrosis factor: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Tumor necrosis factor

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