SMTL ID : 7ndd.1

EM structure of SARS-CoV-2 Spike glycoprotein (one RBD up) in complex with COVOX-159

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: 3 residues within 4Å: Chain A: N.717, L.922, Q.926 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: 4 residues within 4Å: Chain A: E.465 Chain B: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: N.717, L.922, Q.926 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: 3 residues within 4Å: Chain C: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain C: N.717, L.922, Q.926 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)

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

NAG.16: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: N.282 Chain C: K.558 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: N.616, Q.644 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: H.655, N.657 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain A: N.709, I.1130, G.1131 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain A: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain A: N.165 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: E.281, N.282 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain B: N.616 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: H.655, N.657 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: N.709, I.1130, G.1131 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain B: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain B: N.165 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: E.281, N.282 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain C: N.616 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain C: N.709, I.1130, G.1131 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain C: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain C: Q.115, E.132, N.165, T.167 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-159 Fab heavy chain: DFH
COVOX-159 Fab light chain: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

F
F

H
H

E
E

G
G

I
L

Spike glycoprotein

COVOX-159 Fab heavy chain

COVOX-159 Fab light chain

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