SMTL ID : 8dlw.1

Cryo-EM structure of SARS-CoV-2 Epsilon (B.1.429) spike protein in complex with Fab S2M11

Coordinates

PDB Format Compare

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: 3 residues within 4Å: Chain A: C.15, N.17, N.137 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.137 NAG-NAG.2: 4 residues within 4Å: Chain A: N.122, N.125, V.127, E.154 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain B: C.15, N.17, N.137 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.137 NAG-NAG.9: 4 residues within 4Å: Chain B: N.122, N.125, V.127, E.154 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain B: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain E: C.15, N.17, N.137 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.137 NAG-NAG.16: 3 residues within 4Å: Chain E: N.122, N.125, V.127 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 4 residues within 4Å: Chain E: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 3 residues within 4Å: Chain E: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 4 residues within 4Å: Chain E: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 1 residues within 4Å: Chain E: N.1134 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-BMA-FUC.3: 8 residues within 4Å: Chain A: G.339, N.343, V.367 Chain F: F.124 Chain G: S.50, S.51, S.52, G.71 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:S.50 NAG-NAG-BMA-FUC.10: 7 residues within 4Å: Chain B: G.339, N.343, V.367 Chain H: F.124 Chain I: S.50, S.51, S.52 2 PLIP interactions: 1 interactions with chain I, 1 interactions with chain B Hydrogen bonds: I:S.50 Hydrophobic interactions: B:V.367 NAG-NAG-BMA-FUC.17: 6 residues within 4Å: Chain D: S.50, S.51, S.52 Chain E: G.339, N.343, V.367 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.50

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

NAG.22: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: T.108, N.234 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain A: N.164, N.165 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: N.280, N.282 Chain E: K.558 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain A: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain A: N.616 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain A: H.655, N.657 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain A: N.709, G.1131 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain A: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: T.108, N.234 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain B: N.164, N.165 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain A: K.558 Chain B: N.280, N.282 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain B: N.331, Q.580 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain B: N.616 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain B: H.655, N.657 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain B: N.709, G.1131 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain B: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain E: Y.28, N.61 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain E: T.108, N.234 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain E: N.164, N.165 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain B: K.558 Chain E: N.280, N.282 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain E: N.331, Q.580 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain E: N.603 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain E: N.616 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain E: H.655, N.657 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain E: N.709, G.1131 Ligand excluded by PLIP NAG.51: 4 residues within 4Å: Chain E: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mannar, D. et al., SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization. Nat Commun (2022)

Release Date

2022-08-31

Peptides

Spike glycoprotein: ABE
Fab S2M11 heavy chain: CFH
Fab S2M11 light chain: DGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

E
E

C
C

F
F

H
H

D
D

G
G

I
L

Spike glycoprotein

Fab S2M11 heavy chain

Fab S2M11 light chain

Related Entries With Identical Sequence