SMTL ID : 7n0h.1

CryoEM structure of SARS-CoV-2 spike protein (S-6P, 2-up) in complex with sybodies (Sb45)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-mer

Ligands

17 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: 3 residues within 4Å: Chain A: N.331, Q.580, L.582 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: F.342, N.343, S.373 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.373 NAG-NAG.3: 4 residues within 4Å: Chain A: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: K.795, N.801, S.803 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: A.706, E.1072, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain B: A.706, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain C: N.717, L.922, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain C: N.801, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain A: Q.895 Chain C: A.706, E.1072, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain A: C.15, N.17 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain A: N.122, T.124, V.127, E.154 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 1 residues within 4Å: Chain A: N.234 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain B: C.15, N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 1 residues within 4Å: Chain C: N.17 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain C: N.122, T.124, V.127, E.169 No protein-ligand interaction detected (PLIP)

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

NAG.18: 3 residues within 4Å: Chain A: T.307, E.309, N.603 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: F.59, N.61 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: N.616, T.618 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain A: H.146, N.149, S.151 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: E.132, N.165 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: H.655, N.657 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain A: N.709 Chain B: D.796 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain A: N.1134 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain B: Y.28, F.59, S.60, N.61 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: N.616, T.618 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: H.146, N.149 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: E.132, N.165 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: H.655, N.657 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain A: K.558 Chain B: N.282 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain B: S.708, N.709, N.710 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain B: N.1134 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain B: K.558 Chain C: N.282 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain A: N.282, T.284 Chain C: K.558 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: N.331, Q.580 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: G.339, N.343 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain C: H.146, N.149, S.151 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain C: Q.115, E.132, N.165 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain C: N.616 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: H.655, N.657 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain A: D.796 Chain C: N.709 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain C: C.1082, N.1134 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ahmad, J. et al., Structures of synthetic nanobody-SARS-CoV-2 receptor-binding domain complexes reveal distinct sites of interaction. J.Biol.Chem. (2021)

Release Date

2021-06-02

Peptides

Spike glycoprotein: ABC
Synthetic nanobody (Sb45): DE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
X

E
Z

Spike glycoprotein

Synthetic nanobody (Sb45)

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