SMTL ID : 8f4p.1

SARS-CoV-2 spike protein trimer (down conformation) bound with a nanobody

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-mer

Ligands

6 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: 1 residues within 4Å: Chain A: N.330 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 1 residues within 4Å: Chain B: N.1121 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain B: N.1085, T.1087, H.1088, F.1090 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain B: N.704, L.909, Q.913 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain B: N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain B: E.327, N.330 Chain D: G.27, T.28 No protein-ligand interaction detected (PLIP)

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

NAG.7: 1 residues within 4Å: Chain A: N.269 Ligand excluded by PLIP NAG.8: 4 residues within 4Å: Chain A: P.317, N.318, I.319, Q.567 Ligand excluded by PLIP NAG.9: 1 residues within 4Å: Chain A: N.590 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: N.603, C.604 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: N.696, G.1118 Ligand excluded by PLIP NAG.12: 1 residues within 4Å: Chain A: N.704 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: N.1085, G.1086 Ligand excluded by PLIP NAG.14: 1 residues within 4Å: Chain A: N.1121 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain A: N.644 Ligand excluded by PLIP NAG.16: 4 residues within 4Å: Chain A: K.545 Chain B: N.267, E.268, N.269 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain B: N.644 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain B: N.603, T.605 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain B: N.696 Chain C: I.781, D.783 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain B: S.698, N.1061 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain B: N.590 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: N.318, Q.567 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain C: R.315, N.318, Q.567, T.568 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain C: N.590 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain C: H.642, N.644 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain A: D.783 Chain C: N.696, G.1118 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain C: N.704, L.909 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain C: N.1121 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain C: N.330, A.331 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain C: E.268, N.269 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Laughlin, Z.L. et al., SARS-CoV-2 spike protein (down conformation) bound with a nanobody. To Be Published

Release Date

2023-11-15

Peptides

Spike glycoprotein: ABC
Anti-S1 Nanobody: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Spike glycoprotein

Anti-S1 Nanobody

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