SMTL ID : 7akd.1

Structure of the SARS-CoV-2 spike glycoprotein in complex with the 47D11 neutralizing antibody Fab fragment

Coordinates

PDB Format Compare

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)(Non-covalent)

NAG-NAG.1: 2 residues within 4Å: Chain A: N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: G.339, N.343, V.367 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.9: 2 residues within 4Å: Chain B: S.704, N.1074 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.704, B:S.704 NAG-NAG.10: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 7 residues within 4Å: Chain B: R.457, S.459, N.460, K.462, E.465 Chain C: T.108, N.234 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 1 residues within 4Å: Chain C: N.717 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain C: A.706, N.1074 Ligands: FUC.48 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain C: N.1098, H.1101, F.1103 No protein-ligand interaction detected (PLIP)

3 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.2: 2 residues within 4Å: Chain A: E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 2 residues within 4Å: Chain A: N.331, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 2 residues within 4Å: Chain A: K.558 Chain B: N.282 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(3-6)]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.8: 7 residues within 4Å: Chain B: N.343 Chain F: Y.50, G.104 Chain G: N.93, W.94 Ligands: FUC.33, MAN.50 No protein-ligand interaction detected (PLIP)

1 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.12: 3 residues within 4Å: Chain B: K.558 Chain C: E.281, N.282 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- FUC: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-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-MAN-MAN-FUC.13: 9 residues within 4Å: Chain C: N.343, T.345 Chain D: Y.33, G.104, E.105 Chain E: E.1, N.93, W.94 Ligands: MAN-MAN.14 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain C Hydrogen bonds: E:N.93, E:W.94, C:T.345

1 x MAN- MAN: alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose(Non-functional Binders)

MAN-MAN.14: 2 residues within 4Å: Ligands: NAG-NAG-BMA-MAN-MAN-FUC.13, MAN.49 No protein-ligand interaction detected (PLIP)

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

NAG.18: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: N.122, A.123, T.124 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: N.164, N.165 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain A: N.616 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: H.655, N.657 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain A: S.708, N.709 Chain B: I.794, D.796 Ligand excluded by PLIP NAG.24: 5 residues within 4Å: Chain A: N.717, F.718, T.719, A.1070 Ligands: NAG.25 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Ligands: NAG.24 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain A: E.1072, N.1074 Ligands: FUC.27 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain B: N.61 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: N.122, T.124, V.127 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain B: N.165 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain B: T.114, G.232, I.233, N.234 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain B: N.331 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain B: N.616, T.618 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain B: N.709 Chain C: D.796 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain B: N.717 Ligands: NAG.38 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Ligands: NAG.37 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain B: N.801, S.803, Q.804 Ligands: NAG.40 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Ligands: NAG.39 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain C: N.122, T.124 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: N.331, Q.580 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: N.616, T.618 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain C: N.709 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 Ligand excluded by PLIP

3 x FUC: alpha-L-fucopyranose(Non-covalent)

FUC.27: 2 residues within 4Å: Chain A: N.1074 Ligands: NAG.26 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:N.1074 FUC.33: 4 residues within 4Å: Chain B: N.343, T.345 Ligands: NAG-NAG-BMA-MAN-MAN.8, NAG-NAG-BMA-MAN-MAN.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.345 FUC.48: 2 residues within 4Å: Chain C: N.1074 Ligands: NAG-NAG.16 No protein-ligand interaction detected (PLIP)

2 x MAN: alpha-D-mannopyranose(Non-covalent)

MAN.49: 3 residues within 4Å: Chain D: K.64 Ligands: MAN-MAN.14, MAN-MAN.14 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.64 MAN.50: 2 residues within 4Å: Chain F: K.64 Ligands: NAG-NAG-BMA-MAN-MAN.8 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fedry, J. et al., Structural insights into the cross-neutralization of SARS-CoV and SARS-CoV-2 by the human monoclonal antibody 47D11. Sci Adv (2021)

Release Date

2021-05-19

Peptides

Spike glycoprotein: ABC
47D11 neutralizing antibody heavy chain: DF
47D11 neutralizing antibody light chain: EG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

F
H

E
E

G
L

Spike glycoprotein

47D11 neutralizing antibody heavy chain

47D11 neutralizing antibody light chain

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