SMTL ID : 7czf.2 (1 other biounit)

Crystal structure of Kaposi Sarcoma associated herpesvirus (KSHV ) gHgL in complex with the ligand binding domian (LBD) of EphA2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 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: 4 residues within 4Å: Chain B: T.24, N.25, F.38 Chain C: E.82 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain B: N.246, T.248, R.249, L.252 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- MAN- MAN- FUC- FUC: alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN-MAN-FUC-FUC.2: 6 residues within 4Å: Chain A: P.82 Chain B: L.30, N.33, G.34, T.35 Chain C: R.92 No protein-ligand interaction detected (PLIP)

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

NAG.4: 3 residues within 4Å: Chain B: N.104, T.106, F.311 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.311 Hydrogen bonds: B:N.104 NAG.5: 6 residues within 4Å: Chain B: N.188, T.196, S.198, D.237, S.238, Y.239 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.239 Hydrogen bonds: B:N.188, B:D.237, B:Y.239 NAG.6: 5 residues within 4Å: Chain B: N.253, S.257, E.261, T.265, R.269 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.253, B:S.257, B:R.269 NAG.7: 1 residues within 4Å: Chain B: N.344 No protein-ligand interaction detected (PLIP) NAG.8: 2 residues within 4Å: Chain B: R.665, N.667 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.665 NAG.9: 3 residues within 4Å: Chain C: G.100, N.102, T.104 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.102, C:T.104

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Su, C. et al., Molecular basis of EphA2 recognition by gHgL from gammaherpesviruses. Nat Commun (2020)

Release Date

2020-10-21

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

Ephrin type-A receptor 2

Envelope glycoprotein H

Envelope glycoprotein L

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