SMTL ID : 7q0i.1

Crystal structure of the N-terminal domain of SARS-CoV-2 beta variant spike glycoprotein in complex with Beta-43

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

hetero-2-2-2-mer

Ligands

2 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.1: 6 residues within 4Å: Chain C: N.57, N.58, F.59 Chain E: Q.2, C.3, N.5 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain E Hydrophobic interactions: C:N.57, C:F.59, E:Q.2 Hydrogen bonds: C:N.58, E:Q.2, E:C.3, E:N.5 NAG-FUC.3: 4 residues within 4Å: Chain A: Q.13, P.14 Chain E: N.152, N.153 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:N.152 Hydrogen bonds: E:N.153

1 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.2: 8 residues within 4Å: Chain E: N.110, T.112, N.113, V.115, E.142, F.145, Y.148, V.159 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:F.145 Hydrogen bonds: E:Y.148, E:Y.148

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

NAG-NAG.4: 5 residues within 4Å: Chain A: N.57, N.58 Chain F: Q.2, C.3, N.5 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.5: 3 residues within 4Å: Chain F: N.110, T.112, V.115 No protein-ligand interaction detected (PLIP)

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 2 residues within 4Å: Chain A: G.108, Y.109 Ligand excluded by PLIP CL.7: 1 residues within 4Å: Chain A: V.134 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: P.160, E.161, Y.189 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain B: Q.37, G.40, Q.41 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain C: G.108, Y.109, Y.110 Ligand excluded by PLIP CL.14: 5 residues within 4Å: Chain C: E.46, W.47 Chain D: Y.97, V.98, F.99 Ligand excluded by PLIP

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.9: 7 residues within 4Å: Chain A: Y.32, R.98, Y.111, G.112, D.114 Chain B: L.45, Y.48 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.32, A:Y.32, A:G.112, A:G.112

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 7 residues within 4Å: Chain A: K.43, G.44 Chain B: D.84, Y.86, T.101, G.102, K.104 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.86, B:G.102, B:K.104, B:K.104 GOL.12: 8 residues within 4Å: Chain C: Y.158, E.161, P.162, V.163, T.178, P.180, A.181, L.191 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.161, C:V.163, C:A.181 GOL.15: 4 residues within 4Å: Chain D: K.151, D.153, S.154, E.205 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:K.151, D:K.151, D:S.194, D:E.205 Water bridges: D:T.207, D:T.207

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.16: 3 residues within 4Å: Chain D: N.114, P.115, V.204 No protein-ligand interaction detected (PLIP)

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

NAG.17: 3 residues within 4Å: Chain E: T.96, N.222, T.224 No protein-ligand interaction detected (PLIP) NAG.18: 2 residues within 4Å: Chain E: E.266, N.267 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:E.266 NAG.19: 2 residues within 4Å: Chain E: F.47, N.49 No protein-ligand interaction detected (PLIP) NAG.20: 2 residues within 4Å: Chain E: N.137, M.141 No protein-ligand interaction detected (PLIP) NAG.22: 3 residues within 4Å: Chain B: S.66, G.67 Chain F: N.137 No protein-ligand interaction detected (PLIP) NAG.23: 2 residues within 4Å: Chain F: N.152, N.153 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:N.152 Hydrogen bonds: F:N.153 NAG.24: 1 residues within 4Å: Chain F: N.222 No protein-ligand interaction detected (PLIP)

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.21: 6 residues within 4Å: Chain E: I.89, R.90, N.109, V.114, I.116, L.214 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.109

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, C. et al., The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants. Cell Host Microbe (2022)

Release Date

2021-12-22

Peptides

Beta-43 heavy chain: AC
Beta-43 Fab light chain: BD
Spike protein S1: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

C
A

B
L

D
B

E
D

F
C

Beta-43 heavy chain

Beta-43 Fab light chain

Spike protein S1

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