SMTL ID : 7tht.1

CryoEM structure of SARS-CoV-2 S protein in complex with Receptor Binding Domain antibody DH1042

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.42 Å

Oligo State

hetero-3-3-3-mer

Ligands

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 5 residues within 4Å: Chain A: N.691, T.693, L.896, Q.900, Q.1045 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.2: 3 residues within 4Å: Chain A: T.82, N.208, T.210 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain B: N.691, L.896, Q.900, Q.1045 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain C: N.691, L.896, Q.1045 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain A: N.775, S.777 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: N.1072, T.1074, H.1075, F.1077 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 1 residues within 4Å: Chain A: N.1108 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain B: N.775, S.777, Q.778 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain B: N.1072, T.1074, H.1075, F.1077 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 1 residues within 4Å: Chain B: N.1108 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain C: N.775, S.777, Q.778 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain C: N.1072, T.1074, H.1075, F.1077 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 1 residues within 4Å: Chain C: N.1108 No protein-ligand interaction detected (PLIP)

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

NAG.14: 2 residues within 4Å: Chain A: N.256 Chain C: K.532 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain A: N.577 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: N.590, T.592, Q.618 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain A: N.631 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: N.683, I.1104, G.1105 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: A.680, E.1046, N.1048 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: Y.2, N.35 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain A: N.96, T.98, N.99 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: N.305, Q.554 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: F.316, N.317 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain B: N.96 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: T.82, N.208 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain B: N.254, E.255, N.256 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: N.305, Q.554, L.556 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain B: N.577 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: N.590, T.592 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain B: N.631 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain B: N.683, G.1105 Chain C: D.770 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: E.1046, N.1048 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: E.106, N.139 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain B: F.33, N.35 Ligand excluded by PLIP NAG.35: 5 residues within 4Å: Chain B: G.313, F.316, N.317, L.342, F.348 Ligand excluded by PLIP NAG.36: 5 residues within 4Å: Chain C: N.96, N.99, V.101, L.115, V.145 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: G.206, N.208 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: N.254, N.256 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain C: N.305, Q.554, T.555 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: N.577, T.578 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: N.590, T.592 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain C: N.631 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain A: D.770 Chain C: N.683, G.1105 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: E.1046, N.1048 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain C: N.139 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain C: N.35 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gobeil, S.M. et al., Structural diversity of the SARS-CoV-2 Omicron spike. Mol.Cell (2022)

Release Date

2022-02-16

Peptides

Spike glycoprotein: ABC
DH1042 heavy chain: DFH
DH1042 light chain: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
S

B
V

C
C

D
H

F
a

H
d

E
L

G
c

I
b

Spike glycoprotein

DH1042 heavy chain

DH1042 light chain

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