SMTL ID : 8sm0.1

Crystal structure of human complement receptor 2 (CD21) in complex with Epstein-Barr virus major glycoprotein gp350

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

hetero-1-1-mer

Ligands

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

NAG.1: 1 residues within 4Å: Chain A: N.101 No protein-ligand interaction detected (PLIP) NAG.2: 6 residues within 4Å: Chain A: K.57, P.58, G.106, N.107, P.120, T.121 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.106, A:N.107 NAG.4: 5 residues within 4Å: Chain B: D.45, N.47, D.64, Q.133, M.139 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.45 Water bridges: B:N.47 NAG.5: 5 residues within 4Å: Chain B: G.83, G.84, S.85, E.86, N.114 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.84 NAG.6: 7 residues within 4Å: Chain A: R.13 Chain B: N.164, C.165, N.166, D.296, Y.297, C.298 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.166, B:N.166, B:C.298 NAG.7: 5 residues within 4Å: Chain B: E.214, D.215, K.227, F.228, N.229 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.229 NAG.8: 6 residues within 4Å: Chain B: R.273, N.277, V.304, F.305, S.306, D.307 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.307, B:D.307 Water bridges: B:N.277 NAG.9: 7 residues within 4Å: Chain B: M.315, P.316, T.317, N.318, T.414, T.415, T.416 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:P.316, B:N.318, B:T.416 NAG.10: 3 residues within 4Å: Chain B: N.328, S.380, T.392 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.328 NAG.11: 6 residues within 4Å: Chain B: V.7, C.8, Q.9, P.344, N.345, T.410 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:P.344 Water bridges: B:C.8 NAG.12: 3 residues within 4Å: Chain B: A.384, N.386, T.388 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.386, B:T.388, B:T.388 NAG.13: 3 residues within 4Å: Chain B: S.167, T.168, N.169 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.169

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

SO4.3: 2 residues within 4Å: Chain A: Y.80, K.81 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.81 Salt bridges: A:K.81

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, W.-H. et al., Structural Basis For Receptor Engagement And Virus Neutralization Through Epstein-Barr Virus Gp350. To Be Published

Release Date

2024-05-01

Peptides

Complement receptor type 2: A
Envelope glycoprotein gp350: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
G

Complement receptor type 2

Envelope glycoprotein gp350

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