SMTL ID : 7k9j.1

SARS-CoV-2 Spike in complex with neutralizing Fab 2H04 (three down conformation)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

12 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.1: 1 residues within 4Å: Chain A: N.165 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 5 residues within 4Å: Chain A: T.108, N.234 Chain C: K.458, S.459, L.461 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 4 residues within 4Å: Chain A: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 1 residues within 4Å: Chain A: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 1 residues within 4Å: Chain B: N.165 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.16: 5 residues within 4Å: Chain A: K.458, S.459, L.461 Chain B: T.108, N.234 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.27: 4 residues within 4Å: Chain B: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.28: 1 residues within 4Å: Chain B: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.29: 1 residues within 4Å: Chain C: N.165 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.30: 5 residues within 4Å: Chain B: K.458, S.459, L.461 Chain C: T.108, N.234 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.41: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.42: 1 residues within 4Å: Chain C: N.1131 No protein-ligand interaction detected (PLIP)

21 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.3: 3 residues within 4Å: Chain A: N.280, E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.331, Q.580, T.581, L.582 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.582 NAG-NAG.7: 1 residues within 4Å: Chain A: N.616 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain A: H.655, N.657 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain A: N.706, G.1128 Chain B: D.793 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain A: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain A: A.703, E.1069, N.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain B: N.280, E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 4 residues within 4Å: Chain B: N.331, Q.580, T.581, L.582 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.582 NAG-NAG.21: 1 residues within 4Å: Chain B: N.616 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 2 residues within 4Å: Chain B: H.655, N.657 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 3 residues within 4Å: Chain B: N.706, G.1128 Chain C: D.793 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 3 residues within 4Å: Chain B: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 3 residues within 4Å: Chain B: A.703, E.1069, N.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 3 residues within 4Å: Chain C: N.280, E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 4 residues within 4Å: Chain C: N.331, Q.580, T.581, L.582 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:L.582 NAG-NAG.35: 1 residues within 4Å: Chain C: N.616 No protein-ligand interaction detected (PLIP) NAG-NAG.36: 2 residues within 4Å: Chain C: H.655, N.657 No protein-ligand interaction detected (PLIP) NAG-NAG.37: 3 residues within 4Å: Chain A: D.793 Chain C: N.706, G.1128 No protein-ligand interaction detected (PLIP) NAG-NAG.39: 3 residues within 4Å: Chain C: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.40: 3 residues within 4Å: Chain C: A.703, E.1069, N.1071 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-BMA-FUC.5: 11 residues within 4Å: Chain A: F.338, G.339, N.343 Chain C: Y.489 Chain D: W.47, K.59, Y.60, N.61, E.62 Chain G: W.94, P.95 5 PLIP interactions: 1 interactions with chain C, 3 interactions with chain D, 1 interactions with chain G Hydrogen bonds: C:Y.489, D:E.62, D:E.62, D:E.62 Hydrophobic interactions: D:K.59, G:W.94 NAG-NAG-BMA-FUC.19: 9 residues within 4Å: Chain B: F.338, G.339, N.343 Chain E: W.47, K.59, Y.60, E.62 Chain H: W.94, P.95 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain H Hydrogen bonds: E:E.62, E:E.62 Hydrophobic interactions: E:K.59, H:W.94 NAG-NAG-BMA-FUC.33: 10 residues within 4Å: Chain B: Y.489 Chain C: F.338, G.339, N.343 Chain F: W.47, K.59, Y.60, E.62 Chain I: W.94, P.95 4 PLIP interactions: 1 interactions with chain B, 2 interactions with chain F, 1 interactions with chain I Hydrogen bonds: B:Y.489, F:E.62, F:E.62 Hydrophobic interactions: F:K.59, I:W.94

3 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.6: 1 residues within 4Å: Chain A: N.603 No protein-ligand interaction detected (PLIP) NAG-FUC.20: 1 residues within 4Å: Chain B: N.603 No protein-ligand interaction detected (PLIP) NAG-FUC.34: 1 residues within 4Å: Chain C: N.603 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN: 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.10: 3 residues within 4Å: Chain A: N.714, L.919, Q.923 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.919 NAG-NAG-BMA-MAN.24: 3 residues within 4Å: Chain B: N.714, L.919, Q.923 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.919 NAG-NAG-BMA-MAN.38: 3 residues within 4Å: Chain C: N.714, L.919, Q.923 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.919

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

NAG.43: 3 residues within 4Å: Chain A: Y.28, N.30, N.61 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:N.30 NAG.44: 3 residues within 4Å: Chain B: Y.28, N.30, N.61 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:N.30 NAG.45: 3 residues within 4Å: Chain C: Y.28, N.30, N.61 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:N.30

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Errico, J.M. et al., Structural mechanism of SARS-CoV-2 neutralization by two murine antibodies targeting the RBD. Cell Rep (2021)

Release Date

2021-09-29

Peptides

Spike glycoprotein: ABC
2H04 heavy chain: DEF
2H04 light chain: GHI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

E
I

F
J

G
L

H
M

I
N

Spike glycoprotein

2H04 heavy chain

2H04 light chain

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