SMTL ID : 7nd4.1

EM structure of SARS-CoV-2 Spike glycoprotein in complex with COVOX-88 Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

15 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: 1 residues within 4Å: Chain A: N.234 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 1 residues within 4Å: Chain B: N.234 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain B: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 1 residues within 4Å: Chain C: N.234 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain C: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-BMA-MAN-MAN.16: 14 residues within 4Å: Chain C: Q.474, A.475, G.476, S.477, F.486, N.487 Chain D: N.48, R.65, Y.67, N.73, H.113, C.114, S.115, Y.125 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.477, C:S.477, C:Q.474

2 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.17: 13 residues within 4Å: Chain A: A.475, G.476, S.477, F.486, N.487 Chain F: N.48, R.65, Y.67, N.73, H.113, C.114, S.115, Y.125 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.477, A:S.477 NAG-NAG-BMA.18: 12 residues within 4Å: Chain B: A.475, G.476, S.477, N.487 Chain H: N.48, R.65, Y.67, N.73, H.113, C.114, S.115, Y.125 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.477, B:S.477

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

NAG.19: 1 residues within 4Å: Chain A: N.61 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain A: N.122, N.125, V.127, K.129 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: E.281, N.282 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain A: N.331, I.332, Q.580 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain A: N.616, T.618 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: H.655, N.657 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain A: N.709, G.1131 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain A: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain A: Q.115, E.132, N.165 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.61 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain B: N.122, N.125, V.127, K.129 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: E.281, N.282 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain B: N.331, I.332, Q.580 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain B: N.616, T.618 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain B: H.655, N.657 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain B: N.709, G.1131 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain B: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain B: Q.115, E.132, N.165 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain C: N.61 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain C: N.122, N.125, V.127, K.129 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: E.281, N.282 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: N.331, I.332, Q.580 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: N.616, T.618 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain C: H.655, N.657 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain C: N.709, G.1131 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain C: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain C: Q.115, E.132, N.165 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-88 Fab heavy chain: DFH
COVOX-88 Fab light chain: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

F
D

H
F

E
L

G
E

I
G

Spike glycoprotein

COVOX-88 Fab heavy chain

COVOX-88 Fab light chain

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