SMTL ID : 7b7n.1

Human herpesvirus-8 gH/gL in complex with EphA2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.69 Å

Oligo State

hetero-1-1-1-mer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 5 residues within 4Å: Chain B: I.83, N.244, T.246, R.247, L.250 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.83 NAG-NAG.2: 5 residues within 4Å: Chain B: P.612, W.661, R.663, N.665, T.667 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.612

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

CL.3: 3 residues within 4Å: Chain A: G.17, G.20, L.32 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: A.13, I.42, Y.43 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: V.80, R.81, D.82 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain B: F.35 Chain C: R.83 Ligand excluded by PLIP

10 x NA: SODIUM ION(Non-functional Binders)

NA.6: 2 residues within 4Å: Chain A: G.109, T.110 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.109 NA.7: 3 residues within 4Å: Chain A: W.21, Y.45 Chain C: D.50 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.21, A:Y.45 NA.9: 5 residues within 4Å: Chain B: T.52, W.55 Chain C: L.21, F.22 Ligands: NA.18 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:F.22 NA.10: 1 residues within 4Å: Chain B: E.144 No protein-ligand interaction detected (PLIP) NA.11: 2 residues within 4Å: Chain B: T.360, K.361 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.360, B:T.360 NA.12: 2 residues within 4Å: Chain B: T.410, E.415 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.415 NA.13: 1 residues within 4Å: Chain B: L.487 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.487 NA.16: 3 residues within 4Å: Chain B: E.29 Chain C: P.7, H.29 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.29 NA.17: 1 residues within 4Å: Chain C: A.94 No protein-ligand interaction detected (PLIP) NA.18: 3 residues within 4Å: Chain B: T.52 Chain C: F.23 Ligands: NA.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.52

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

NAG.8: 2 residues within 4Å: Chain B: N.23, F.36 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.23 NAG.14: 2 residues within 4Å: Chain C: N.100, T.102 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.102

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Light, T.P. et al., Human herpesvirus 8 molecular mimicry of ephrin ligands facilitates cell entry and triggers EphA2 signaling. Plos Biol. (2021)

Release Date

2020-12-30

Peptides

Ephrin type-A receptor 2: A
Envelope glycoprotein H: B
Envelope glycoprotein L: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
H

C
L

Ephrin type-A receptor 2

Envelope glycoprotein H

Envelope glycoprotein L