SMTL ID : 7vnd.1

Structure of the SARS-CoV-2 spike glycoprotein in complex with a human single domain antibody n3113 (UUD-state, state 2)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-mer

Ligands

16 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: T.95, N.221 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.704, L.909, Q.913 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: N.788, S.790 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain A: N.1085, T.1087, H.1088, F.1090, Y.1097 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain B: T.95, N.221 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 1 residues within 4Å: Chain B: N.269 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain B: A.693, N.1061 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain B: N.1085, T.1087, H.1088, F.1090 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.1088 NAG-NAG.9: 1 residues within 4Å: Chain B: N.1121 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain B: N.704, F.705, L.909, Q.913 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain B: N.788, S.790, Q.791 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.791 NAG-NAG.12: 4 residues within 4Å: Chain A: K.545 Chain C: N.267, E.268, N.269 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain C: N.704, L.909, Q.1058 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.909 NAG-NAG.14: 2 residues within 4Å: Chain C: K.1060, N.1061 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.1061 NAG-NAG.15: 3 residues within 4Å: Chain C: N.1085, T.1087, H.1088 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.1088 NAG-NAG.16: 2 residues within 4Å: Chain C: N.318, Q.567 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.318

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

NAG.17: 4 residues within 4Å: Chain A: Y.15, F.46, S.47, N.48 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: N.318, Q.567 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain A: N.644 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: N.696, N.697, G.1118 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: A.693, N.1061 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: Y.15, F.46, N.48 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: H.133, N.136 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain B: N.318, Q.567, L.569 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain B: N.644 Ligand excluded by PLIP NAG.27: 5 residues within 4Å: Chain B: N.109, T.111, N.112, V.114, E.143 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: N.603, T.605 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain C: Y.15, F.46, N.48 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain C: N.136 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain C: N.644 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain C: N.788, S.790 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain C: N.109, A.110, T.111, N.112 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain C: T.95, N.221 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain B: D.783 Chain C: N.696, N.697 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain C: N.603, T.605, Q.631 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, Z. et al., A non-ACE2 competing human single-domain antibody confers broad neutralization against SARS-CoV-2 and circulating variants. Signal Transduct Target Ther (2021)

Release Date

2021-11-24

Peptides

Spike glycoprotein: ABC
n3113: DE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

C
C

D
V

E
D

Spike glycoprotein

n3113

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