SMTL ID : 7ndb.1

EM structure of SARS-CoV-2 Spike glycoprotein in complex with COVOX-253H165L Fab

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-1-mer

Ligands

10 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: 3 residues within 4Å: Chain A: N.234, T.236 Chain C: K.462 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.717, L.922, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.922 NAG-NAG.3: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain B: N.801, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain C: N.717, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain C: N.801, S.803, Q.804, Q.935 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-FUC.11: 7 residues within 4Å: Chain B: S.477 Chain D: H.113, N.115, T.117, S.118, C.119, Y.120 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.118 Hydrophobic interactions: D:Y.120

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

NAG.12: 2 residues within 4Å: Chain A: N.280, N.282 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: N.331, Q.580 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain A: F.338, G.339, F.342, N.343 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: E.309, N.603, T.604 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain A: N.616 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: N.709, G.1131 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain A: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain B: F.59, N.61 Ligand excluded by PLIP NAG.22: 6 residues within 4Å: Chain A: R.457, K.462, E.465 Chain B: T.108, N.234, T.236 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: E.281, N.282 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain B: N.331, P.579, Q.580, L.582 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: N.616, E.619 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: H.655, N.657 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain B: N.709, N.710, G.1131 Chain C: D.796 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain B: N.717, L.922, Q.926, Q.1071 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain B: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.30: 5 residues within 4Å: Chain B: F.338, G.339, F.342, N.343, L.368 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain C: N.280, N.282 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain C: N.331, Q.580, T.581 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain C: N.616 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: N.709, G.1131 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain C: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain C: N.1134 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: G.339, N.343 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dejnirattisai, W. et al., The antigenic anatomy of SARS-CoV-2 receptor binding domain. Cell (2021)

Release Date

2021-03-03

Peptides

Spike glycoprotein: ABC
COVOX-253H165L Fab heavy chain: D
COVOX-253H165L Fab light chain: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

E
L

Spike glycoprotein

COVOX-253H165L Fab heavy chain

COVOX-253H165L Fab light chain

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