SMTL ID : 7kp7.1

asymmetric mTNF-alpha hTNFR1 complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

hetero-3-3-mer

Ligands

30 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 3 residues within 4Å: Chain A: K.94, D.95 Chain B: K.103 Ligand excluded by PLIP SO4.2: 3 residues within 4Å: Chain A: L.35, K.36, D.37 Ligand excluded by PLIP SO4.3: 6 residues within 4Å: Chain A: K.89, E.107 Chain B: K.89, E.107 Chain C: K.89, E.107 Ligand excluded by PLIP SO4.4: 3 residues within 4Å: Chain B: K.94, D.95 Chain C: K.103 Ligand excluded by PLIP SO4.5: 3 residues within 4Å: Chain B: L.35, K.36, D.37 Ligand excluded by PLIP SO4.6: 3 residues within 4Å: Chain B: Q.23 Chain D: Y.27, Y.29 Ligand excluded by PLIP SO4.7: 6 residues within 4Å: Chain B: R.73, S.77, Q.116, E.118 Chain F: L.56, R.57 Ligand excluded by PLIP SO4.8: 3 residues within 4Å: Chain A: K.103 Chain C: K.94, D.95 Ligand excluded by PLIP SO4.9: 3 residues within 4Å: Chain C: L.35, K.36, D.37 Ligand excluded by PLIP SO4.10: 6 residues within 4Å: Chain C: R.73, S.77, Q.116, E.118 Chain E: L.56, R.57 Ligand excluded by PLIP SO4.11: 5 residues within 4Å: Chain D: I.74, G.86, C.87, R.93, E.120 Ligand excluded by PLIP SO4.12: 6 residues within 4Å: Chain A: R.73, S.77, Q.116, E.118 Chain D: L.56, R.57 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain D: Q.71, V.72, E.73 Ligand excluded by PLIP SO4.14: 3 residues within 4Å: Chain D: Y.92, H.94, N.123 Ligand excluded by PLIP SO4.15: 4 residues within 4Å: Chain D: C.128, F.132, F.133, L.134 Ligand excluded by PLIP SO4.16: 4 residues within 4Å: Chain D: Q.6, G.7, K.21, E.53 Ligand excluded by PLIP SO4.17: 3 residues within 4Å: Chain D: I.74, S.75, S.76 Ligand excluded by PLIP SO4.18: 4 residues within 4Å: Chain D: V.84, R.93, Y.95, K.121 Ligand excluded by PLIP SO4.21: 1 residues within 4Å: Chain E: R.81 Ligand excluded by PLIP SO4.22: 3 residues within 4Å: Chain E: Y.92, H.94, N.123 Ligand excluded by PLIP SO4.23: 1 residues within 4Å: Chain E: H.115 Ligand excluded by PLIP SO4.24: 3 residues within 4Å: Chain E: C.128, F.133, L.134 Ligand excluded by PLIP SO4.25: 3 residues within 4Å: Chain E: I.74, S.75, S.76 Ligand excluded by PLIP SO4.28: 5 residues within 4Å: Chain F: I.74, G.86, C.87, R.93, E.120 Ligand excluded by PLIP SO4.29: 1 residues within 4Å: Chain F: R.81 Ligand excluded by PLIP SO4.30: 3 residues within 4Å: Chain F: Y.92, H.94, N.123 Ligand excluded by PLIP SO4.31: 1 residues within 4Å: Chain F: H.115 Ligand excluded by PLIP SO4.32: 4 residues within 4Å: Chain F: Q.6, G.7, K.21, E.53 Ligand excluded by PLIP SO4.33: 3 residues within 4Å: Chain F: I.74, S.75, S.76 Ligand excluded by PLIP SO4.34: 3 residues within 4Å: Chain F: V.84, C.85, R.93 Ligand excluded by PLIP

5 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.19: 1 residues within 4Å: Chain D: N.111 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.111, D:N.111 NAG.20: 2 residues within 4Å: Chain B: E.101 Chain D: N.105 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:E.101 Hydrogen bonds: D:N.105 NAG.26: 2 residues within 4Å: Chain E: N.111, F.132 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.111 NAG.27: 2 residues within 4Å: Chain A: E.101 Chain E: N.105 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: A:E.101 Hydrogen bonds: E:N.105 NAG.35: 2 residues within 4Å: Chain C: E.101 Chain F: N.105 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain C Hydrogen bonds: F:N.105 Hydrophobic interactions: C:E.101

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McMillan, D. et al., Structural insights into the disruption of TNF-TNFR1 signalling by small molecules stabilising a distorted TNF. Nat Commun (2021)

Release Date

2021-01-13

Peptides

Tumor necrosis factor: ABC
Tumor necrosis factor receptor superfamily member 1A: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

C
C

D
E

E
D

F
F

Tumor necrosis factor

Tumor necrosis factor receptor superfamily member 1A

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