SMTL ID : 6z43.1

Cryo-EM Structure of SARS-CoV-2 Spike : H11-D4 Nanobody Complex

Coordinates

PDB Format Compare

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: 3 residues within 4Å: Chain A: N.122, V.127, V.171 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.127 NAG-NAG.2: 3 residues within 4Å: Chain A: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: N.280, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain A: N.331, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain A: N.717, F.718, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain B: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Q.804 Hydrogen bonds: B:S.803 NAG-NAG.11: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.1101 NAG-NAG.12: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain C: N.122, T.124, V.127, V.171 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.171 NAG-NAG.14: 3 residues within 4Å: Chain C: N.280, E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain C: N.709, I.1130, G.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 5 residues within 4Å: Chain C: T.716, N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 5 residues within 4Å: Chain B: Q.895 Chain C: S.704, A.706, E.1072, N.1074 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.704 NAG-NAG.19: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 2 residues within 4Å: Chain C: D.1127, N.1134 No protein-ligand interaction detected (PLIP)

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

NAG.21: 2 residues within 4Å: Chain A: F.59, N.61 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: N.616, T.618 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: N.709, G.1131 Chain C: D.796 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain A: A.706, E.1072, N.1074 Chain C: Q.895 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain A: E.132, N.165 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain A: N.343, V.367, L.368 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.61 Ligand excluded by PLIP NAG.30: 5 residues within 4Å: Chain B: N.122, T.124, N.125, V.127, V.171 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain B: N.282 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: N.331, Q.580 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain B: N.616 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain B: N.709, I.1130 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain B: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain B: G.339, N.343 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: N.343, V.367 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain C: N.61 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain C: N.234 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain C: N.331, Q.580 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: N.616, T.618 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain A: Y.396 Chain C: N.165 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huo, J. et al., Structural basis for a potent neutralising single-domain antibody that blocks SARS-CoV-2 binding to its receptor ACE2. To Be Published

Release Date

2020-06-03

Peptides

Spike glycoprotein: ABC
Nanobody: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
X

E
Y

F
Z

Spike glycoprotein

Nanobody

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