SMTL ID : 6zdh.1

SARS-CoV-2 Spike glycoprotein in complex with a neutralizing antibody EY6A Fab

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

13 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: 6 residues within 4Å: Chain A: T.716, N.717, L.922, N.925, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.922 NAG-NAG.2: 5 residues within 4Å: Chain A: K.795, N.801, S.803, Q.804, Q.935 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain A: N.1098, G.1099, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain A: V.1133, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain B: T.716, N.717, L.922, N.925, Q.926 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain B: K.795, N.801, S.803, Q.804, Q.935 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain B: N.1098, G.1099, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain C: N.331, T.333, Q.580, T.581 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 5 residues within 4Å: Chain C: T.716, N.717, L.922, N.925, Q.926 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.922 NAG-NAG.11: 5 residues within 4Å: Chain C: N.801, S.803, Q.804, F.817, Q.935 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 5 residues within 4Å: Chain C: N.1098, G.1099, T.1100, H.1101, F.1103 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.1101 NAG-NAG.13: 3 residues within 4Å: Chain C: I.1132, V.1133, N.1134 No protein-ligand interaction detected (PLIP)

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

NAG.14: 4 residues within 4Å: Chain A: Y.28, F.59, S.60, N.61 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: N.234 Chain C: H.519 Ligand excluded by PLIP NAG.16: 4 residues within 4Å: Chain A: N.280, E.281, N.282 Chain C: K.558 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain A: N.331, T.333, Q.580, T.581 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: N.616, T.618 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: H.655, V.656, N.657 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: N.709, I.1130, G.1131 Ligand excluded by PLIP NAG.21: 5 residues within 4Å: Chain A: A.706, E.1072, K.1073, N.1074 Chain B: Q.895 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain B: Y.28, F.59, S.60, N.61 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: H.519 Chain B: N.234 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain A: K.558 Chain B: N.280, N.282 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain B: N.331, T.333, Q.580, T.581 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain B: N.616, T.618, Q.644 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: H.655, N.657 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain B: N.709, I.1130, G.1131 Chain C: D.796 Ligand excluded by PLIP NAG.29: 5 residues within 4Å: Chain B: A.706, E.1072, K.1073, N.1074 Chain C: Q.895 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain C: Y.28, F.59, S.60, N.61 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: H.519 Chain C: N.234 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain C: N.280, E.281, N.282 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: N.616, T.618 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain C: N.709, I.1130, G.1131 Ligand excluded by PLIP NAG.36: 5 residues within 4Å: Chain A: Q.895 Chain C: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, D. et al., Structural basis for the neutralization of SARS-CoV-2 by an antibody from a convalescent patient. Nat.Struct.Mol.Biol. (2020)

Release Date

2020-07-01

Peptides

Spike glycoprotein: ABC
EY6A heavy chain: DFH
EY6A light chain: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

F
D

H
G

E
L

G
F

I
I

Spike glycoprotein

EY6A heavy chain

EY6A light chain

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