SMTL ID : 7l09.1

Cryo-EM structure of SARS-CoV-2 2P S ectodomain bound domain-swapped antibody 2G12 from masked 3D refinement

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-2-mer

Ligands

10 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: 2 residues within 4Å: Chain A: V.1107, N.1108 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.1072, T.1074, H.1075, F.1077 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain B: N.691, L.896, Q.900 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.896 NAG-NAG.6: 3 residues within 4Å: Chain B: N.775, S.777, Q.778 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain B: N.1072, T.1074, H.1075, F.1077 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain B: N.1108 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain C: N.691, L.896, Q.900 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.896 NAG-NAG.10: 3 residues within 4Å: Chain C: N.775, S.777, Q.778 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain C: N.1072, T.1074, H.1075, F.1077 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain C: N.1108 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-BMA-MAN-MAN.2: 10 residues within 4Å: Chain A: N.775, S.777, Q.778 Chain D: S.55, T.56, Y.57, R.58 Chain G: R.28, L.75, E.76 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:R.28, G:R.28, G:R.28, G:R.28, G:R.28

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

NAG-NAG-BMA-MAN-MAN-MAN-BMA-BMA.3: 25 residues within 4Å: Chain A: N.691, F.692, T.693, L.896, N.899, Q.900, Q.1045 Chain E: G.93, Y.94 Chain G: A.31, H.32, T.33, S.52, T.53, S.54, T.56, Y.57, K.99, G.100, S.101, L.104, S.105, D.106, N.107, D.108 10 PLIP interactions: 1 interactions with chain A, 8 interactions with chain G, 1 interactions with chain E Hydrophobic interactions: A:Q.900 Hydrogen bonds: G:H.32, G:T.33, G:T.33, G:T.33, G:K.99, G:S.105, G:D.108, G:D.108, E:Y.94

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

NAG-NAG-BMA-MAN-BMA.13: 7 residues within 4Å: Chain A: I.768 Chain C: N.683 Chain D: A.31, T.33, T.53, D.106 Chain F: Y.94 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:A.31, D:T.33, D:T.33, D:T.53

32 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.14: 2 residues within 4Å: Chain A: S.34, N.35 Ligand excluded by PLIP NAG.15: 6 residues within 4Å: Chain A: N.96, A.97, T.98, N.99, V.101, K.103 Ligand excluded by PLIP NAG.16: 4 residues within 4Å: Chain A: P.304, N.305, P.553, Q.554 Ligand excluded by PLIP NAG.17: 7 residues within 4Å: Chain A: F.312, G.313, F.316, N.317, V.341, L.342, F.348 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.577 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain A: A.680, E.1046, K.1047, N.1048 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: E.106, N.139 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: H.629, N.631 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain A: N.254, E.255, N.256 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: N.590, T.592 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain A: N.683, N.684 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain B: N.254, E.255, N.256 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain B: P.304, N.305, P.553, Q.554 Ligand excluded by PLIP NAG.27: 6 residues within 4Å: Chain B: F.312, G.313, F.316, N.317, V.341, L.342 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, Q.618 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: H.629, N.631 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain B: N.683, I.1104, G.1105 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain B: A.680, E.1046, K.1047, N.1048 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: E.106, N.139 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain B: N.35 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain B: N.96, A.97, N.99, K.103 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: H.629, N.631 Ligand excluded by PLIP NAG.37: 5 residues within 4Å: Chain A: Q.869 Chain C: A.680, E.1046, K.1047, N.1048 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: E.106, N.139 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain C: N.35 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain C: N.96, A.97, N.99, K.103 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain C: N.254, E.255, N.256 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain C: P.304, N.305, P.553, Q.554 Ligand excluded by PLIP NAG.43: 6 residues within 4Å: Chain C: F.312, G.313, F.316, N.317, V.341, L.342 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain C: N.577 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain C: N.590, Q.618 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Williams, W.B. et al., Fab-dimerized glycan-reactive antibodies are a structural category of natural antibodies. Cell (2021)

Release Date

2020-12-30

Peptides

Spike glycoprotein: ABC
2G12 heavy chain: DG
2G12 light chain: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

G
M

E
K

F
L

Spike glycoprotein

2G12 heavy chain

2G12 light chain

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