SMTL ID : 7kml.1

cryo-EM structure of SARS-CoV-2 spike in complex with Fab 15033-7, three RBDs bound

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

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.1: 5 residues within 4Å: Chain A: N.122, A.123, T.124, N.125, V.126 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: N.280, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain A: S.708, N.709, N.710, G.1131 Chain C: D.796 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.710 NAG-NAG.6: 5 residues within 4Å: Chain A: N.717, T.719, L.922, N.925, Q.926 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.925, A:Q.926 Hydrogen bonds: A:N.925 NAG-NAG.7: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.804 NAG-NAG.8: 5 residues within 4Å: Chain A: N.703, S.704, V.705, A.706, N.1074 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.704 NAG-NAG.9: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 5 residues within 4Å: Chain B: N.122, A.123, T.124, N.125, V.126 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain B: N.280, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 5 residues within 4Å: Chain A: D.796 Chain B: S.708, N.709, N.710, G.1131 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.710 NAG-NAG.15: 5 residues within 4Å: Chain B: N.717, T.719, L.922, N.925, Q.926 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:N.925, B:Q.926 Hydrogen bonds: B:N.925 NAG-NAG.16: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.804 NAG-NAG.17: 5 residues within 4Å: Chain B: N.703, S.704, V.705, A.706, N.1074 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.704 NAG-NAG.18: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 5 residues within 4Å: Chain C: N.122, A.123, T.124, N.125, V.126 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 2 residues within 4Å: Chain C: N.280, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 5 residues within 4Å: Chain B: D.796 Chain C: S.708, N.709, N.710, G.1131 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.710 NAG-NAG.24: 5 residues within 4Å: Chain C: N.717, T.719, L.922, N.925, Q.926 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:N.925, C:Q.926 Hydrogen bonds: C:N.925 NAG-NAG.25: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.804 NAG-NAG.26: 5 residues within 4Å: Chain C: N.703, S.704, V.705, A.706, N.1074 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.704 NAG-NAG.27: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP)

6 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.3: 2 residues within 4Å: Chain A: N.331, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 5 residues within 4Å: Chain A: F.342, N.343, V.367, S.371, S.373 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 2 residues within 4Å: Chain B: N.331, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 5 residues within 4Å: Chain B: F.342, N.343, V.367, S.371, S.373 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.21: 2 residues within 4Å: Chain C: N.331, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.22: 5 residues within 4Å: Chain C: F.342, N.343, V.367, S.371, S.373 No protein-ligand interaction detected (PLIP)

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

NAG.28: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain A: Q.115, E.132, N.165, T.167 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain A: G.232, N.234 Chain B: H.519 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain A: N.616, T.618 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.33: 5 residues within 4Å: Chain A: C.1082, N.1125, C.1126, D.1127, N.1134 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain B: Q.115, E.132, N.165, T.167 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain B: G.232, N.234 Chain C: H.519 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain B: N.616, T.618 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.39: 5 residues within 4Å: Chain B: C.1082, N.1125, C.1126, D.1127, N.1134 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain C: Q.115, E.132, N.165, T.167 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain A: H.519 Chain C: G.232, N.234 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: N.616, T.618 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.45: 5 residues within 4Å: Chain C: C.1082, N.1125, C.1126, D.1127, N.1134 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miersch, S. et al., Tetravalent SARS-CoV-2 Neutralizing Antibodies Show Enhanced Potency and Resistance to Escape Mutations. J.Mol.Biol. (2021)

Release Date

2021-02-10

Peptides

Spike glycoprotein: ABC
Fab 15033-7 light chain: DFH
Fab 15033-7 heavy chain: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
L

F
M

H
N

E
H

G
I

I
J

Spike glycoprotein

Fab 15033-7 light chain

Fab 15033-7 heavy chain

Related Entries With Identical Sequence