SMTL ID : 7mw4.1

Structure of the SARS-CoV-2 Spike trimer with one RBD down in complex with the Fab fragment of human neutralizing antibody clone 6

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

3 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 4 residues within 4Å: Chain A: N.331, Q.580, T.581, L.582 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain A: N.343, V.367, S.371, S.373 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 2 residues within 4Å: Chain G: N.343, V.367 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.2: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: N.717, L.922, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.922 NAG-NAG.6: 4 residues within 4Å: Chain A: N.709, N.710, G.1131 Chain D: D.796 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 1 residues within 4Å: Chain A: N.234 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 1 residues within 4Å: Chain D: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain D: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain D: N.801, S.803 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain D: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain D: N.709, G.1131 Chain G: D.796 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 2 residues within 4Å: Chain D: T.108, N.234 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain D: G.339, N.343, V.367 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain G: N.331, Q.580, L.582 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 1 residues within 4Å: Chain G: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 4 residues within 4Å: Chain G: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 3 residues within 4Å: Chain G: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 4 residues within 4Å: Chain G: N.717, L.922, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:L.922 NAG-NAG.21: 2 residues within 4Å: Chain G: N.709, G.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 3 residues within 4Å: Chain G: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP)

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

NAG.24: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: N.616, T.618 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain A: E.309, N.603 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain A: E.132, N.164, N.165 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain A: E.281, N.282 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain A: N.122, A.123, N.125 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain A: A.706, E.1072, N.1074 Ligands: NAG.32 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain A: N.1074, F.1075 Ligands: NAG.31 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain D: N.657 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain D: N.616, T.618, Q.644 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain D: N.603, T.604 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain D: N.164, N.165 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain D: Y.28, N.30, N.61 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain D: E.281, N.282 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain D: N.122, V.127 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain D: N.331, Q.580, T.581 Ligand excluded by PLIP NAG.41: 5 residues within 4Å: Chain D: A.706, E.1072, K.1073, N.1074 Ligands: NAG.42 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain D: N.1074 Ligands: NAG.41 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain G: N.657 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain G: N.616, T.618 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain G: N.603 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain G: N.164, N.165 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain G: Y.28, N.30, N.61 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain G: E.281, N.282 Ligand excluded by PLIP NAG.49: 4 residues within 4Å: Chain G: N.122, T.124, N.125, V.127 Ligand excluded by PLIP NAG.50: 5 residues within 4Å: Chain A: Q.895 Chain G: A.706, E.1072, N.1074 Ligands: NAG.51 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain G: N.1074 Ligands: NAG.50 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Peng, L. et al., Monospecific and bispecific monoclonal SARS-CoV-2 neutralizing antibodies that maintain potency against B.1.617. Nat Commun (2022)

Release Date

2022-03-16

Peptides

Spike glycoprotein: ADG
Fab of antibody clone 6, light chain: BEH
Fab of antibody clone 6, heavy chain: CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

D
A

G
B

B
L

E
E

H
G

C
H

F
D

I
F

Spike glycoprotein

Fab of antibody clone 6, light chain

Fab of antibody clone 6, heavy chain

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