SMTL ID : 7vnc.1

Structure of the SARS-CoV-2 spike glycoprotein in complex with a human single domain antibody n3113 (UDD-state, state 1)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-mer

Ligands

3 x NAG- NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-NAG.1: 3 residues within 4Å: Chain A: E.119, N.151, N.152 No protein-ligand interaction detected (PLIP) NAG-NAG-NAG.7: 2 residues within 4Å: Chain C: N.151, N.152 No protein-ligand interaction detected (PLIP) NAG-NAG-NAG.11: 4 residues within 4Å: Chain C: I.455 Chain D: E.119, N.151, N.152 No protein-ligand interaction detected (PLIP)

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.2: 4 residues within 4Å: Chain A: S.691, A.693, N.1061 Chain C: Q.882 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 1 residues within 4Å: Chain A: N.1121 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 6 residues within 4Å: Chain A: N.704, F.705, T.706, L.909, Q.913, Q.1058 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain A: N.788, S.790 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: N.1085, T.1087, H.1088, F.1090 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain A: K.545 Chain C: E.268, N.269 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 1 residues within 4Å: Chain C: N.1121 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain C: N.1085, T.1087, H.1088, F.1090 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain D: N.1121 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain D: N.704, L.909, N.912, Q.1058 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.912 NAG-NAG.14: 2 residues within 4Å: Chain D: N.788, S.790 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain D: N.1085, T.1087, H.1088, F.1090 No protein-ligand interaction detected (PLIP)

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

NAG.16: 1 residues within 4Å: Chain A: N.330 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: N.318, Q.567 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: N.696, G.1118 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain C: N.330 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain C: Y.15, F.46, N.48 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain C: N.318 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain C: N.590 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain C: N.603, T.605 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain C: N.644 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain C: N.696 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain C: N.704, Q.913, Q.1058 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain C: N.788, S.790, Q.791 Ligand excluded by PLIP NAG.28: 7 residues within 4Å: Chain D: F.325, G.326, E.327, V.328, F.329, N.330, L.355 Ligand excluded by PLIP NAG.29: 6 residues within 4Å: Chain D: Q.1, C.2, N.4, C.123, N.124, D.125 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain D: N.48 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain D: N.318 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain A: D.783 Chain D: N.696, G.1118 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain A: Q.882 Chain D: N.1061 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: ACD
n3113: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

C
A

D
B

B
V

Spike glycoprotein

n3113

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