SMTL ID : 7uz5.1

Structure of the SARS-CoV-2 S 6P trimer in complex with the mouse antibody Fab fragment, M8a-6

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-1-mer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: Y.28, F.59, S.60, N.61 Ligand excluded by PLIP NAG.2: 4 residues within 4Å: Chain A: N.122, T.124, N.125, V.127 Ligand excluded by PLIP NAG.3: 2 residues within 4Å: Chain A: Q.115, N.165 Ligand excluded by PLIP NAG.4: 3 residues within 4Å: Chain A: G.232, I.233, N.234 Ligand excluded by PLIP NAG.5: 3 residues within 4Å: Chain A: N.280, N.282 Chain B: K.558 Ligand excluded by PLIP NAG.6: 2 residues within 4Å: Chain A: N.331, Q.580 Ligand excluded by PLIP NAG.7: 3 residues within 4Å: Chain A: G.339, F.342, N.343 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain A: N.603, T.604 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain A: N.616, T.618, Q.644 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: H.655, N.657 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: N.706, G.1128 Chain C: D.793 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: N.714, L.919, Q.923 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain A: N.798, S.800, Q.801 Ligand excluded by PLIP NAG.14: 6 residues within 4Å: Chain A: V.702, A.703, A.710, N.1071 Chain C: A.890, Q.892 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain A: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: I.1129, N.1131 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain B: N.122, T.124, E.154, F.157 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain B: E.132, N.165 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain B: N.234 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain B: E.281, N.282 Chain C: K.558 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain B: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: G.339, N.343, V.367 Ligand excluded by PLIP NAG.24: 5 residues within 4Å: Chain B: T.307, K.310, G.601, N.603, T.604 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain B: N.616 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain A: D.793 Chain B: N.706, N.707, G.1128 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: N.714, L.919, Q.923 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: N.798, Q.801 Ligand excluded by PLIP NAG.30: 6 residues within 4Å: Chain A: A.890, Q.892 Chain B: A.703, A.710, E.1069, N.1071 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain B: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain B: N.1131 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.34: 5 residues within 4Å: Chain C: N.122, T.124, N.125, V.127, E.154 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain A: L.518 Chain C: Q.115, N.165 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain C: N.234 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: E.281, N.282 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: N.331, Q.580 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: N.343, S.373 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain C: G.601, N.603, T.604 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain C: N.616, T.618, Q.644 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: N.706, G.1128 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain C: N.714, L.919, Q.923 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain C: N.798, S.800 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain C: A.703, E.1069, N.1071 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain C: N.1131 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fan, C. et al., Neutralizing monoclonal antibodies elicited by mosaic RBD nanoparticles bind conserved sarbecovirus epitopes. Immunity (2022)

Release Date

2022-12-07

Peptides

Spike glycoprotein: ABC
M8a-6 Fab heavy chain: D
M8a-6 Fab light chain: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

E
L

Spike glycoprotein

M8a-6 Fab heavy chain

M8a-6 Fab light chain

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