SMTL ID : 7uz4.1

Structure of the SARS-CoV-2 S 6P trimer in complex with the mouse antibody Fab fragment, M8a-3

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-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 4 residues within 4Å: Chain A: N.714, L.919, Q.923, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain B: N.714, L.919, Q.923, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain C: N.714, L.919, Q.923, Q.1068 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.919

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

NAG.4: 2 residues within 4Å: Chain A: N.331, Q.580 Ligand excluded by PLIP NAG.5: 3 residues within 4Å: Chain A: N.603, T.604, P.939 Ligand excluded by PLIP NAG.6: 1 residues within 4Å: Chain A: N.616 Ligand excluded by PLIP NAG.7: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain A: N.706, G.1128 Chain B: D.793 Ligand excluded by PLIP NAG.9: 4 residues within 4Å: Chain A: A.703, E.1069, K.1070, N.1071 Ligand excluded by PLIP NAG.10: 4 residues within 4Å: Chain A: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.11: 1 residues within 4Å: Chain A: N.1131 Ligand excluded by PLIP NAG.12: 5 residues within 4Å: Chain A: F.338, G.339, F.342, N.343, S.371 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.14: 6 residues within 4Å: Chain A: V.120, N.122, T.124, N.125, V.127, F.157 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain A: Q.115, E.132, N.165, T.167 Ligand excluded by PLIP NAG.16: 5 residues within 4Å: Chain A: N.196, G.199, G.232, I.233, N.234 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: N.280, E.281, N.282 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: N.798, S.800, Q.801 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain B: N.331, Q.580, T.581 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain B: N.603, T.604 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain B: N.616, Q.644 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: N.706, G.1128 Chain C: D.793 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain B: A.703, E.1069, K.1070, N.1071 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain B: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain B: N.1131 Ligand excluded by PLIP NAG.27: 5 residues within 4Å: Chain B: F.338, G.339, F.342, N.343, S.371 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.29: 5 residues within 4Å: Chain B: N.122, A.123, T.124, N.125, E.154 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: Q.115, E.132, N.165 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain B: N.234 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: E.281, N.282 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain B: N.798, S.800, Q.801 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain C: N.331, Q.580, L.582 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain C: E.309, N.603, T.604 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: N.616, T.618 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain A: D.793 Chain C: N.706, G.1128 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain C: A.703, E.1069, K.1070, N.1071 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain C: N.1131 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain C: N.343 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: F.59, N.61 Ligand excluded by PLIP NAG.44: 6 residues within 4Å: Chain C: V.120, N.122, T.124, N.125, E.154, F.157 Ligand excluded by PLIP NAG.45: 5 residues within 4Å: Chain C: Q.115, E.132, N.165, C.166, T.167 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain C: N.234 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain B: K.558 Chain C: N.280, E.281, N.282 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain C: N.798, S.800, N.925 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-3 Fab heavy chain: DFH
M8a-3 Fab light chain: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

F
M

H
P

E
L

G
N

I
Q

Spike glycoprotein

M8a-3 Fab heavy chain

M8a-3 Fab light chain

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