SMTL ID : 7kpb.1

Human TNF-alpha TNFR1 complex bound to conformationally selective antibody

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-3-2-1-1-mer

Ligands

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 4 residues within 4Å: Chain A: Q.26, L.27, E.136, I.137 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.27, A:I.137 GOL.2: 5 residues within 4Å: Chain B: Q.26, L.27, E.136, I.137, P.140 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.27, B:I.137 GOL.3: 2 residues within 4Å: Chain B: N.138, R.139 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Y.95 GOL.5: 8 residues within 4Å: Chain B: R.32, R.33 Chain D: Y.27, C.44, E.45, S.48, H.58, C.59 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:E.45, D:S.48, D:H.58, B:R.33 GOL.6: 8 residues within 4Å: Chain B: E.147 Chain C: T.80, N.93, S.96, I.98 Chain D: S.97, N.99 Ligands: GOL.7 7 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C, 4 interactions with chain D Hydrogen bonds: B:E.147, C:N.93, C:S.96, D:S.97, D:S.97, D:N.99, D:N.99 GOL.7: 6 residues within 4Å: Chain C: E.136, I.137, N.138 Chain D: S.97, E.98 Ligands: GOL.6 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:E.98, C:E.136 GOL.9: 7 residues within 4Å: Chain A: R.32 Chain E: Y.27, E.45, S.48, R.57, H.58, C.59 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:E.45, E:E.45, E:S.48, E:C.59 GOL.10: 3 residues within 4Å: Chain E: C.41, R.42, E.43 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:C.41, E:E.43 GOL.11: 5 residues within 4Å: Chain A: L.76, I.98 Chain F: Y.49, A.55, D.56 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:Y.49, F:D.56

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)

D84.4: 26 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, 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 18 PLIP interactions: 9 interactions with chain A, 7 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: A:L.58, A:L.58, A:L.58, A:Y.120, A:V.124, A:L.158, 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:K.12 pi-Stacking: C:Y.60, C:Y.120, C:Y.120

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

NAG.8: 1 residues within 4Å: Chain E: N.111 No protein-ligand interaction detected (PLIP)

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
Tumor necrosis factor receptor superfamily member 1A: DE
Fab1974 - Light Chain: F
Fab1974 - Heavy Chain: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
F

E
E

F
L

G
H

Tumor necrosis factor

Tumor necrosis factor receptor superfamily member 1A

Fab1974 - Light Chain

Fab1974 - Heavy Chain

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