SMTL ID : 8eyh.1

SARS-CoV-2 spike protein bound with a nanobody

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-3-mer

Ligands

5 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: 1 residues within 4Å: Chain B: N.1121 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain B: N.1085, G.1086, T.1087, H.1088 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain B: T.703, N.704, Q.1058 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain B: N.788, N.915 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain B: P.324, F.325, G.326, F.329, N.330 No protein-ligand interaction detected (PLIP)

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

NAG.6: 4 residues within 4Å: Chain B: N.267, E.268, N.269, T.271 Ligand excluded by PLIP NAG.7: 1 residues within 4Å: Chain B: N.644 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain B: N.603, T.605 Ligand excluded by PLIP NAG.9: 2 residues within 4Å: Chain B: N.696 Chain C: P.884 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain B: N.1061 Chain C: P.879, A.880 Ligand excluded by PLIP NAG.11: 1 residues within 4Å: Chain B: N.590 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain B: N.318, Q.567 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain C: N.318, S.517 Ligand excluded by PLIP NAG.14: 1 residues within 4Å: Chain C: N.590 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain C: N.644 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain C: N.696 Chain D: P.884 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain C: N.704, Q.1058 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain C: N.1121 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain C: N.330, V.354, N.357, W.423 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain D: E.268, N.269 Ligand excluded by PLIP NAG.22: 5 residues within 4Å: Chain D: N.318, N.321, L.322, P.566, Q.567 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain D: T.294, N.590 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain D: N.603, C.604 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain D: N.696, I.1117 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain D: N.704, Q.1058 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain D: N.1085 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain D: N.1121 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain D: G.326, N.330 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Laughlin, Z.L. et al., SARS-CoV-2 spike protein bound with nanobody. To Be Published

Release Date

2023-11-01

Peptides

Nanobody: A
Spike glycoprotein: BCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
B

C
C

D
A

Nanobody

Spike glycoprotein

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