SMTL ID : 7vne.1

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

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

20 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.267, N.269 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 1 residues within 4Å: Chain A: N.1121 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.704, Q.913, Q.1058 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain A: N.1085, T.1087, H.1088, F.1090, Y.1097 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain A: N.318, Q.567 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain A: K.545 Chain C: E.268, N.269 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.545, A:K.545 NAG-NAG.9: 4 residues within 4Å: Chain C: A.693, E.1059, N.1061 Chain E: Q.882 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 1 residues within 4Å: Chain C: N.1121 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain C: N.696 Chain E: D.783 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain C: N.704, Q.913 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain C: N.1085, T.1087, H.1088, F.1090 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain C: N.318, Q.567, T.568, L.569 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain E: T.95, T.96, N.221, T.223 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain C: K.545 Chain E: E.268, N.269 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 3 residues within 4Å: Chain A: Q.882 Chain E: A.693, N.1061 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 1 residues within 4Å: Chain E: N.1121 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 2 residues within 4Å: Chain A: D.783 Chain E: N.696 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 3 residues within 4Å: Chain E: N.704, L.909, Q.1058 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:L.909 NAG-NAG.22: 4 residues within 4Å: Chain E: N.1085, T.1087, H.1088, F.1090 No protein-ligand interaction detected (PLIP)

2 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.7: 1 residues within 4Å: Chain C: N.152 No protein-ligand interaction detected (PLIP) NAG-NAG-NAG.15: 4 residues within 4Å: Chain E: K.100, E.119, N.151, N.152 No protein-ligand interaction detected (PLIP)

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

NAG.23: 2 residues within 4Å: Chain A: G.326, N.330 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain A: Q.1, C.2, N.4 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: Y.15, N.48 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain A: N.136 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain A: N.644 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain A: A.693, E.1059, N.1061 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain A: N.696, N.697, G.1118 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain A: N.603, T.605, Q.631 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain C: N.330 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain C: N.17, N.48 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain C: H.133, N.135, N.136 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain C: N.644 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: N.788, S.790 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain E: G.326, F.329, N.330, S.358 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain E: Y.15, N.48 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain E: H.133, N.136 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain E: H.642, N.644 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain E: N.788, S.790, Q.791 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain E: P.317, N.318, T.320, Q.567 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain E: N.603, T.605 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: ACE
n3113.1: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

C
A

E
B

B
W

D
U

F
V

Spike glycoprotein

n3113.1

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