SMTL ID : 7l06.1

Cryo-EM structure of SARS-CoV-2 2P S ectodomain bound to two copies of domain-swapped antibody 2G12

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-4-4-mer

Ligands

8 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.6: 4 residues within 4Å: Chain C: N.691, L.896, N.899, Q.900 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.896 NAG-NAG.7: 3 residues within 4Å: Chain C: N.775, S.777, Q.778 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain C: N.1072, G.1073, T.1074, H.1075, F.1077 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.1075 NAG-NAG.9: 2 residues within 4Å: Chain C: V.1107, N.1108 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 1 residues within 4Å: Chain B: N.1108 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain B: N.1072, T.1074, H.1075, F.1077 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.1075

2 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: 11 residues within 4Å: Chain A: K.769, N.775, S.777, Q.778 Chain H: S.55, T.56, Y.57, R.58 Chain K: R.28, L.75, E.76 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:R.28, K:R.28, K:R.28, K:R.28, K:R.28 NAG-NAG-BMA-MAN-MAN.12: 10 residues within 4Å: Chain B: 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

2 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: 24 residues within 4Å: Chain A: N.691, F.692, T.693, L.896, N.899, Q.900, Q.1045 Chain I: G.93, Y.94 Chain K: A.31, H.32, T.33, S.52, T.53, S.54, T.56, Y.57, K.99, G.100, L.104, S.105, D.106, N.107, D.108 10 PLIP interactions: 2 interactions with chain A, 1 interactions with chain I, 7 interactions with chain K Hydrophobic interactions: A:L.896, A:Q.900 Hydrogen bonds: I:Y.94, K:T.33, K:T.33, K:T.33, K:K.99, K:S.105, K:D.108, K:D.108 NAG-NAG-BMA-MAN-MAN-MAN-BMA-BMA.13: 24 residues within 4Å: Chain B: 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, L.104, S.105, D.106, N.107, D.108 10 PLIP interactions: 2 interactions with chain B, 1 interactions with chain E, 7 interactions with chain G Hydrophobic interactions: B:L.896, B:Q.900 Hydrogen bonds: E:Y.94, G:T.33, G:T.33, G:T.33, G:K.99, G:S.105, G:D.108, G:D.108

2 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.5: 8 residues within 4Å: Chain A: N.683, I.1104 Chain B: I.768, D.770 Chain D: T.33, T.53, D.106 Chain F: Y.94 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.33, D:T.33, D:T.53 NAG-NAG-BMA-MAN-BMA.10: 10 residues within 4Å: Chain A: I.768, D.770 Chain C: N.683, I.1104, G.1105 Chain H: T.33, T.53, S.105, D.106 Chain J: Y.94 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:D.106

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

NAG.15: 2 residues within 4Å: Chain A: S.34, N.35 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: 5 residues within 4Å: Chain A: A.680, E.1046, K.1047, N.1048 Chain B: Q.869 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: H.629, N.631 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain A: N.254, E.255, N.256 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain A: N.590, C.591, T.592 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: S.34, N.35 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain B: P.304, N.305, P.553, Q.554 Ligand excluded by PLIP NAG.25: 7 residues within 4Å: Chain B: F.312, G.313, F.316, N.317, V.341, L.342, F.348 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain B: N.577 Ligand excluded by PLIP NAG.27: 5 residues within 4Å: Chain B: A.680, E.1046, K.1047, N.1048 Chain C: Q.869 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: H.629, N.631 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: N.254, E.255, N.256 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: N.590, C.591, T.592 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: N.683, N.684 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain C: H.629, V.630, N.631 Ligand excluded by PLIP NAG.33: 5 residues within 4Å: Chain A: Q.869 Chain C: A.680, E.1046, K.1047, N.1048 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain C: S.34, N.35 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain C: N.254, E.255, N.256 Ligand excluded by PLIP NAG.36: 5 residues within 4Å: Chain C: P.304, N.305, P.553, Q.554, T.555 Ligand excluded by PLIP NAG.37: 7 residues within 4Å: Chain C: F.312, G.313, F.316, N.317, V.341, L.342, F.348 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain C: N.577 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain C: N.590, T.592, 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: DGHK
2G12 light chain: EFIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

G
G

H
H

K
M

E
E

F
F

I
K

J
L

Spike glycoprotein

2G12 heavy chain

2G12 light chain

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