SMTL ID : 7akj.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

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.1: 2 residues within 4Å: Chain A: N.92, E.114 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain A: S.88, T.89, S.94, N.210 Chain B: R.427 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain A: N.252 Chain B: R.527 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: Y.761, N.766, S.768, Q.769 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain B: N.92, E.114 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain B: S.88, T.89, S.94, N.210 Chain G: R.427 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain B: N.252 Chain G: R.527 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain B: Y.761, N.766, S.768, Q.769 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 2 residues within 4Å: Chain G: N.92, E.114 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 5 residues within 4Å: Chain A: R.427 Chain G: S.88, T.89, S.94, N.210 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 2 residues within 4Å: Chain A: R.527 Chain G: N.252 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 4 residues within 4Å: Chain G: Y.761, N.766, S.768, Q.769 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-FUC.2: 5 residues within 4Å: Chain A: N.102, S.103, T.104, N.105, Q.130 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.105 NAG-NAG-FUC.8: 5 residues within 4Å: Chain B: N.102, S.103, T.104, N.105, Q.130 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.105 NAG-NAG-FUC.14: 5 residues within 4Å: Chain G: N.102, S.103, T.104, N.105, Q.130 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:N.105

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- FUC: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-[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-MAN-MAN-MAN-FUC.5: 12 residues within 4Å: Chain A: N.313, T.315, I.411 Chain C: Y.33, Y.50, N.58, K.64, G.104, E.105 Chain D: E.1, N.93, P.95 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.58 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-FUC.11: 12 residues within 4Å: Chain B: N.313, T.315, I.411 Chain E: Y.33, Y.50, N.58, K.64, G.104, E.105 Chain F: E.1, N.93, P.95 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.58 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-FUC.17: 12 residues within 4Å: Chain G: N.313, T.315, I.411 Chain H: Y.33, Y.50, N.58, K.64, G.104, E.105 Chain I: E.1, N.93, P.95 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:N.58

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

NAG.19: 3 residues within 4Å: Chain A: Q.15, N.48, T.50 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain A: N.56 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain A: F.140, N.141 Chain B: I.438 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain A: N.301 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain A: S.336, V.337, N.340 Chain D: S.31 Ligand excluded by PLIP NAG.24: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: N.585, T.587 Chain G: L.814 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain A: N.674 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain A: N.682, Q.887 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain A: T.676, N.1039 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain A: N.1063, T.1065, F.1068 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain A: N.1099 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain B: Q.15, N.48, T.50 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain B: N.56 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain B: F.140, N.141 Chain G: I.438 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain B: N.301 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain B: S.336, V.337, N.340 Chain F: S.31 Ligand excluded by PLIP NAG.36: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain A: L.814 Chain B: N.585, T.587 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain B: N.674 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain B: N.682, Q.887 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain B: T.676, N.1039 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain B: N.1063, T.1065, F.1068 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain B: N.1099 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain G: Q.15, N.48, T.50 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain G: N.56 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain A: I.438 Chain G: F.140, N.141 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain G: N.301 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain G: S.336, V.337, N.340 Chain I: S.31 Ligand excluded by PLIP NAG.48: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain B: L.814 Chain G: N.585, T.587 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain G: N.674 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain G: N.682, Q.887 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain G: T.676, N.1039 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain G: N.1063, T.1065, F.1068 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain G: N.1099 Ligand excluded by 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: ABG
47D11 neutralizing antibody heavy chain: CEH
47D11 neutralizing antibody light chain: DFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
B

G
A

C
G

E
E

H
H

D
F

F
D

I
L

Spike glycoprotein

47D11 neutralizing antibody heavy chain

47D11 neutralizing antibody light chain

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