SMTL ID : 8dm3.1

Cryo-EM structure of SARS-CoV-2 Omicron BA.2 spike protein in complex with Fab 4A8

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

18 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.119, T.121, N.122, V.124, E.151 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.714, L.919, Q.923, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: A.703, E.1069, N.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 1 residues within 4Å: Chain A: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain B: N.119, T.121, N.122, V.124, E.151 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain B: N.714, L.919, Q.923, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain B: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain B: S.701, A.703, E.1069, N.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain B: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain B: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 5 residues within 4Å: Chain C: N.119, T.121, N.122, E.151, V.168 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:V.168 Hydrogen bonds: C:N.122 NAG-NAG.14: 4 residues within 4Å: Chain C: N.714, L.919, Q.923, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain C: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain C: A.703, E.1069, N.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 1 residues within 4Å: Chain C: N.1131 No protein-ligand interaction detected (PLIP)

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

NAG.19: 2 residues within 4Å: Chain A: Y.25, N.58 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain A: N.162 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain A: T.105, N.231, T.233 Chain C: E.462 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain A: N.277, E.278, N.279 Chain C: K.555 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: N.328, P.576, Q.577 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain A: D.336, N.340 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: N.706, G.1128 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: Y.25, N.58 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain B: N.162 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: T.105, N.231, T.233 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain A: K.555 Chain B: N.277, E.278, N.279 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain B: N.328, P.576, Q.577, L.579 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain B: N.340 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: N.706, G.1128 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: Y.25, N.58 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain C: N.162 Ligand excluded by PLIP NAG.35: 7 residues within 4Å: Chain B: R.454, L.458, K.459, E.462 Chain C: T.105, N.231, T.233 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain B: K.555 Chain C: E.278, N.279 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain C: N.328, P.576, Q.577 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: D.336, N.340 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: N.706, G.1128 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saville, J.W. et al., Structural analysis of receptor engagement and antigenic drift within the BA.2 spike protein. Cell Rep (2023)

Release Date

2023-01-25

Peptides

Spike glycoprotein: ABC
Fab 4A8 heavy chain: DFH
Fab 4A8 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

Fab 4A8 heavy chain

Fab 4A8 light chain

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