SMTL ID : 4rsu.1 (2 other biounits)

Crystal structure of the light and hvem complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-6-6-mer

Ligands

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

CL.1: 6 residues within 4Å: Chain A: R.153, D.154, G.155, T.156, R.157, S.158 Ligand excluded by PLIP CL.2: 3 residues within 4Å: Chain A: R.97 Chain D: L.54, S.55 Ligand excluded by PLIP CL.3: 6 residues within 4Å: Chain B: R.153, D.154, G.155, T.156, R.157, S.158 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain B: G.44 Chain D: R.26, K.56, C.57 Ligand excluded by PLIP CL.6: 6 residues within 4Å: Chain C: R.153, D.154, G.155, T.156, R.157, S.158 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain C: R.97 Chain F: L.54, S.55 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain B: R.97 Chain E: L.54, S.55, K.56 Ligand excluded by PLIP CL.14: 6 residues within 4Å: Chain G: R.153, D.154, G.155, T.156, R.157, S.158 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain G: R.97 Chain J: L.54, S.55 Ligand excluded by PLIP CL.17: 4 residues within 4Å: Chain G: L.43, G.44 Chain L: K.56, C.57 Ligand excluded by PLIP CL.18: 6 residues within 4Å: Chain H: R.153, D.154, G.155, T.156, R.157, S.158 Ligand excluded by PLIP CL.20: 6 residues within 4Å: Chain I: R.153, D.154, G.155, T.156, R.157, S.158 Ligand excluded by PLIP CL.24: 5 residues within 4Å: Chain I: L.43, G.44 Chain K: R.26, K.56, C.57 Ligand excluded by PLIP CL.26: 3 residues within 4Å: Chain I: R.97 Chain L: L.54, S.55 Ligand excluded by PLIP

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain B: L.102, E.103 Chain C: L.45, D.154, T.156 Chain E: L.58, Q.59 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B, 1 interactions with chain E Hydrogen bonds: C:D.154, B:E.103, E:Q.59 Water bridges: C:L.45 GOL.7: 9 residues within 4Å: Chain A: S.125, S.126, F.127 Chain B: S.125, S.126, F.127 Chain C: S.125, S.126, F.127 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 2 interactions with chain C Hydrogen bonds: A:F.127, B:F.127, C:F.127, C:F.127 GOL.9: 7 residues within 4Å: Chain A: L.102, E.103 Chain B: L.45, D.154, T.156 Chain D: L.58, Q.59 5 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: D:Q.59, D:Q.59, A:E.103 Water bridges: D:Q.59, B:D.154 GOL.13: 7 residues within 4Å: Chain A: L.45, D.154, T.156 Chain C: L.102, E.103 Chain F: L.58, Q.59 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C, 1 interactions with chain F Hydrogen bonds: A:D.154, F:Q.59 Water bridges: A:L.45, C:E.103 GOL.16: 7 residues within 4Å: Chain G: L.102, E.103 Chain H: L.45, D.154, T.156 Chain J: L.58, Q.59 5 PLIP interactions: 2 interactions with chain G, 2 interactions with chain H, 1 interactions with chain J Hydrogen bonds: G:E.103, H:D.154, J:Q.59 Water bridges: G:E.103, H:L.45 GOL.19: 6 residues within 4Å: Chain H: L.102, E.103 Chain I: L.45, D.154, T.156 Chain K: Q.59 4 PLIP interactions: 2 interactions with chain I, 2 interactions with chain K Hydrogen bonds: I:D.154, K:Q.59 Water bridges: I:G.44, K:C.57 GOL.21: 9 residues within 4Å: Chain G: S.125, S.126, F.127 Chain H: S.125, S.126, F.127 Chain I: S.125, S.126, F.127 8 PLIP interactions: 3 interactions with chain G, 3 interactions with chain I, 2 interactions with chain H Hydrogen bonds: G:S.125, G:F.127, I:F.127, H:F.127, H:F.127 Water bridges: G:S.125, I:S.126, I:F.127 GOL.22: 5 residues within 4Å: Chain G: D.154 Chain I: L.102, E.103 Chain L: L.58, Q.59 6 PLIP interactions: 2 interactions with chain G, 1 interactions with chain I, 3 interactions with chain L Water bridges: G:D.154, G:D.154, L:Q.59, L:Q.59 Hydrogen bonds: I:E.103, L:Q.59

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

NAG.10: 3 residues within 4Å: Chain D: R.70, S.72, N.74 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.74, D:N.74 NAG.12: 3 residues within 4Å: Chain E: A.71, S.72, N.74 No protein-ligand interaction detected (PLIP) NAG.23: 4 residues within 4Å: Chain J: R.70, A.71, S.72, N.74 No protein-ligand interaction detected (PLIP) NAG.25: 4 residues within 4Å: Chain K: A.71, S.72, R.73, N.74 No protein-ligand interaction detected (PLIP) NAG.27: 4 residues within 4Å: Chain L: R.70, A.71, S.72, N.74 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, W. et al., HVEM structures and mutants reveal distinct functions of binding to LIGHT and BTLA/CD160. J.Exp.Med. (2021)

Release Date

2015-02-04

Peptides

Tumor necrosis factor ligand superfamily member 14, soluble form: ABCGHI
Tumor necrosis factor receptor superfamily member 14: DEFJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

G
G

H
H

I
I

D
D

E
E

F
F

J
J

K
K

L
L

Tumor necrosis factor ligand superfamily member 14, soluble form

Tumor necrosis factor receptor superfamily member 14

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