SMTL ID : 7z7x.1

CRYO-EM STRUCTURE OF SARS-COV-2 SPIKE : H11-H6 nanobody complex

Coordinates

PDB Format

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: 4 residues within 4Å: Chain A: N.122, V.127, E.169, V.171 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.280, N.282 Chain B: K.558 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: N.331, P.579, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: N.717, L.922, 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: 3 residues within 4Å: Chain B: N.717, L.922, Q.1071 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.922 NAG-NAG.10: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 5 residues within 4Å: Chain C: N.122, T.124, V.127, K.129, V.171 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain C: N.280, E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 2 residues within 4Å: Chain C: N.709, I.1130 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain C: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 2 residues within 4Å: Chain C: N.801, S.803 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 3 residues within 4Å: Chain C: A.706, E.1072, N.1074 No protein-ligand interaction detected (PLIP) 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: 1 residues within 4Å: Chain C: 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: 3 residues within 4Å: Chain A: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain A: N.164, N.165 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain A: F.338, F.342, N.343, L.368 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: N.122, V.127 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: N.280, 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: 3 residues within 4Å: Chain A: D.796 Chain B: N.709, G.1131 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain B: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain B: F.338, G.339, N.343 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain C: F.338, G.339, N.343 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: Y.28, 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: 1 residues within 4Å: Chain C: N.616 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain C: N.165 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mikolajek, H. et al., Correlation between the binding affinity and the conformational entropy of nanobody SARS-CoV-2 spike protein complexes. Proc.Natl.Acad.Sci.USA (2022)

Release Date

2022-07-13

Peptides

Spike glycoprotein,Fibritin: ABC
Nanobody H11-H6: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
F

E
D

F
E

Spike glycoprotein,Fibritin

Nanobody H11-H6

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