SMTL ID : 8gnh.1

Complex structure of BD-218 and Spike protein

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-1-mer

Ligands

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

NAG-NAG.1: 3 residues within 4Å: Chain B: N.331, Q.580, T.581 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain C: K.795, N.801, S.803 No protein-ligand interaction detected (PLIP)

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

NAG.3: 1 residues within 4Å: Chain A: N.801 Ligand excluded by PLIP NAG.4: 2 residues within 4Å: Chain A: N.1098, T.1100 Ligand excluded by PLIP NAG.5: 1 residues within 4Å: Chain A: Y.28 Ligand excluded by PLIP NAG.6: 2 residues within 4Å: Chain A: K.129, A.163 Ligand excluded by PLIP NAG.7: 4 residues within 4Å: Chain A: N.280, E.281, N.282 Chain C: K.558 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain A: N.331, Q.580 Ligand excluded by PLIP NAG.9: 2 residues within 4Å: Chain A: N.343, F.374 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: N.603, T.604 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: N.616, T.618 Chain B: R.847 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: H.655, N.657 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain A: N.709 Ligand excluded by PLIP NAG.14: 1 residues within 4Å: Chain A: N.1074 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain B: N.1098, H.1101 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain B: N.717, L.922, Q.1071 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain B: N.1134 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain B: G.339, N.343 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain B: Y.28, F.59, N.61, P.631 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain B: E.281, N.282, T.286 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain B: T.307, N.603 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain B: N.616 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: H.655, N.657 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: N.709, G.1131 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: N.164, N.165 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain C: T.716, N.717, L.922 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain C: N.1134 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain C: N.61 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain C: N.280, E.281, N.282 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain C: N.331, Q.580 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain C: N.616 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain A: D.796 Chain C: N.709 Ligand excluded by PLIP NAG.34: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, B. et al., Human antibody BD-218 has broad neutralizing activity against concerning variants of SARS-CoV-2. Int.J.Biol.Macromol. (2023)

Release Date

2023-08-30

Peptides

Spike glycoprotein: ABC
Heavy chain of BD-218: D
Light chain of BD-218: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

E
L

Spike glycoprotein

Heavy chain of BD-218

Light chain of BD-218

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