SMTL ID : 8slr.1

Crystal Structure of mouse TRAIL

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-trimer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 14 residues within 4Å: Chain A: C.124, W.125, S.126 Chain B: C.124, W.125, S.126 Chain C: C.124, W.125, S.126 Ligands: CL.2, ZN.7, CL.8, ZN.13, CL.14 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C Metal complexes: A:C.124, B:C.124, C:C.124 ZN.7: 14 residues within 4Å: Chain A: C.124, W.125, S.126 Chain B: C.124, W.125, S.126 Chain C: C.124, W.125, S.126 Ligands: ZN.1, CL.2, CL.8, ZN.13, CL.14 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C Metal complexes: A:C.124, B:C.124, C:C.124 ZN.13: 14 residues within 4Å: Chain A: C.124, W.125, S.126 Chain B: C.124, W.125, S.126 Chain C: C.124, W.125, S.126 Ligands: ZN.1, CL.2, ZN.7, CL.8, CL.14 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C Metal complexes: A:C.124, B:C.124, C:C.124

9 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 8 residues within 4Å: Chain A: C.124 Chain B: C.124 Chain C: C.124 Ligands: ZN.1, ZN.7, CL.8, ZN.13, CL.14 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain A: K.98, Q.99, N.156 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain A: R.79, L.159, M.160, D.161 Ligand excluded by PLIP CL.8: 8 residues within 4Å: Chain A: C.124 Chain B: C.124 Chain C: C.124 Ligands: ZN.1, CL.2, ZN.7, ZN.13, CL.14 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain B: K.98, Q.99, N.156 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain B: R.79, L.159, M.160, D.161 Ligand excluded by PLIP CL.14: 8 residues within 4Å: Chain A: C.124 Chain B: C.124 Chain C: C.124 Ligands: ZN.1, CL.2, ZN.7, CL.8, ZN.13 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain C: K.98, Q.99, N.156 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain C: R.79, L.159, M.160, D.161 Ligand excluded by PLIP

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 9 residues within 4Å: Chain A: K.106, T.108, Y.110, I.114, K.145 Chain C: R.46, K.47, G.48, H.49 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:R.46, C:H.49, A:K.106 PEG.11: 9 residues within 4Å: Chain A: R.46, K.47, G.48, H.49 Chain B: K.106, T.108, Y.110, I.114, K.145 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.46, A:H.49, B:K.106 PEG.17: 9 residues within 4Å: Chain B: R.46, K.47, G.48, H.49 Chain C: K.106, T.108, Y.110, I.114, K.145 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:R.46, B:H.49, C:K.106

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 4 residues within 4Å: Chain A: G.36, Q.37, T.155, N.156 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.156 Water bridges: A:G.36, A:Q.37, A:E.157 EDO.12: 4 residues within 4Å: Chain B: G.36, Q.37, T.155, N.156 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.156 Water bridges: B:G.36, B:Q.37, B:E.157 EDO.18: 4 residues within 4Å: Chain C: G.36, Q.37, T.155, N.156 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.156 Water bridges: C:G.36, C:Q.37, C:E.157

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Luo, Y. et al., Heparan sulfate promotes TRAIL-induced tumor cell apoptosis. Elife (2024)

Release Date

2024-04-03

Peptides

Tumor necrosis factor ligand superfamily member 10: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
D

C
D

Tumor necrosis factor ligand superfamily member 10