SMTL ID : 7nd7.1

EM structure of SARS-CoV-2 Spike glycoprotein in complex with COVOX-316 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: 8 residues within 4Å: Chain A: T.108, N.234, T.236, R.237 Chain C: R.457, S.459, K.462, E.465 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.459, C:S.459 NAG-NAG.2: 2 residues within 4Å: Chain A: N.717, L.922 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: 8 residues within 4Å: Chain A: R.457, S.459, K.462, E.465 Chain B: T.108, N.234, T.236, R.237 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain B: N.717, L.922 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: 10 residues within 4Å: Chain B: R.457, K.458, S.459, N.460, K.462, E.465 Chain C: T.108, N.234, T.236, R.237 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.459 NAG-NAG.12: 2 residues within 4Å: Chain C: N.717, L.922 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: 2 residues within 4Å: Chain C: I.1132, N.1134 No protein-ligand interaction detected (PLIP)

3 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.16: 11 residues within 4Å: Chain A: T.478, P.479, C.480, N.481, V.483, F.486, C.488 Chain D: T.58, N.59 Chain E: S.96, N.97 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:P.479, A:N.481, E:N.97 NAG-NAG-FUC.17: 11 residues within 4Å: Chain B: T.478, P.479, C.480, N.481, V.483, F.486, C.488 Chain F: T.58, N.59 Chain G: S.96, N.97 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.479, B:N.481 NAG-NAG-FUC.18: 9 residues within 4Å: Chain C: P.479, C.480, N.481, V.483, F.486 Chain H: T.58, N.59 Chain I: S.96, N.97 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:P.479, C:N.481

25 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: 3 residues within 4Å: Chain A: N.122, N.125, V.127 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: E.281, N.282 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: N.331, Q.580 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain A: N.616 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain A: H.655, N.657 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: N.709, I.1130 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain A: E.132, N.165 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain B: N.61 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: N.122, N.125, V.127 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.282 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: N.331, Q.580 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain B: N.616 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: H.655, N.657 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: N.709, I.1130 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain B: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain A: I.468 Chain B: E.132, N.165 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain C: N.61 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain C: N.122, N.125, V.127 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: N.280, E.281, N.282 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: N.331, Q.580 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain C: N.616 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain C: N.709 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain B: I.468, T.470 Chain C: 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-316 Fab heavy chain: DFH
COVOX-316 Fab light chain: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

F
F

H
J

E
L

G
G

I
K

Spike glycoprotein

COVOX-316 Fab heavy chain

COVOX-316 Fab light chain

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