SMTL ID : 7kmk.1

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

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-2-mer

Ligands

7 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: N.122, A.123, T.124, N.125, V.127, M.153, E.169, V.171 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.171 NAG-NAG.4: 5 residues within 4Å: Chain B: N.717, L.922, N.925, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.922 NAG-NAG.5: 2 residues within 4Å: Chain B: N.801, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 6 residues within 4Å: Chain A: Q.895 Chain B: S.704, V.705, A.706, E.1072, N.1074 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.706 NAG-NAG.7: 6 residues within 4Å: Chain C: N.122, T.124, N.125, V.127, M.153, V.171 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.171 NAG-NAG.8: 3 residues within 4Å: Chain C: N.717, L.922, Q.926 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP)

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.2: 5 residues within 4Å: Chain A: N.331, P.579, Q.580, T.581, L.582 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 3 residues within 4Å: Chain B: N.331, Q.580, L.582 No protein-ligand interaction detected (PLIP)

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

NAG.10: 2 residues within 4Å: Chain A: E.281, N.282 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: G.339, F.342, N.343 Ligand excluded by PLIP NAG.12: 5 residues within 4Å: Chain A: D.614, V.615, N.616, Q.644, T.645 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain A: N.709, I.1130 Chain C: D.796 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain A: N.717, L.922, Q.926, Q.1071 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: G.799, F.800, N.801 Ligand excluded by PLIP NAG.16: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain A: C.1082, G.1085, C.1126, N.1134 Ligand excluded by PLIP NAG.18: 8 residues within 4Å: Chain B: N.122, A.123, T.124, N.125, V.127, W.152, M.153, V.171 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain B: N.280, E.281, N.282 Ligand excluded by PLIP NAG.20: 6 residues within 4Å: Chain B: F.342, N.343, L.368, S.371, S.373, W.436 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain B: V.615, N.616, Q.644, R.646 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: V.656, N.657 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: N.709, I.1130, G.1131 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain B: N.1098, G.1099, Y.1110 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: C.1082, N.1134 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain C: K.113, Q.115, N.165 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain C: E.281, N.282 Ligand excluded by PLIP NAG.28: 6 residues within 4Å: Chain C: G.339, F.342, N.343, L.368, S.371, S.373 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain C: N.616, E.619 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain C: H.655, N.657 Ligand excluded by PLIP NAG.31: 5 residues within 4Å: Chain B: D.796 Chain C: S.708, N.709, N.710, I.1130 Ligand excluded by PLIP NAG.32: 5 residues within 4Å: Chain B: Q.895 Chain C: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, I.1114 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain C: C.1082, C.1126, 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: DF
Fab 15033-7 heavy chain: EG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
L

F
M

E
H

G
I

Spike glycoprotein

Fab 15033-7 light chain

Fab 15033-7 heavy chain

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