SMTL ID : 7r4q.1

The SARS-CoV-2 spike in complex with the 1.29 neutralizing nanobody

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-mer

Ligands

5 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Non-functional Binders)(Post Translational Modification)

NAG-NAG.1: 3 residues within 4Å: Chain A: V.16, N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain C: N.122, T.124, N.125, V.127, E.154, V.171 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain C: C.15, V.16, N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 10 residues within 4Å: Chain B: R.454, R.457, K.458, K.462, E.465, D.467, S.469 Chain C: T.108, N.234, T.236 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.457, B:R.457, B:D.467

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

NAG.6: 5 residues within 4Å: Chain A: H.146, N.148, N.149, S.151, M.153 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain A: N.164, N.165 Ligand excluded by PLIP NAG.8: 5 residues within 4Å: Chain A: N.280, E.281, N.282 Chain C: K.558, L.560 Ligand excluded by PLIP NAG.9: 5 residues within 4Å: Chain A: N.331, P.579, Q.580, T.581, L.582 Ligand excluded by PLIP NAG.10: 4 residues within 4Å: Chain A: N.343, S.371, S.373, F.374 Ligand excluded by PLIP NAG.11: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain A: N.616, T.618, Q.644, R.646 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: V.656, N.657 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain A: N.709, N.710, G.1131 Chain B: I.794 Ligand excluded by PLIP NAG.16: 5 residues within 4Å: Chain A: T.716, N.717, L.922, Q.926, Q.1071 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: A.706, N.1074, N.1098 Ligand excluded by PLIP NAG.18: 5 residues within 4Å: Chain A: N.1098, G.1099, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: V.1133, N.1134 Ligand excluded by PLIP NAG.20: 7 residues within 4Å: Chain B: N.122, T.124, N.125, V.127, K.129, E.154, V.171 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain B: H.146, M.153 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain B: N.165 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: N.280, E.281, N.282 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain B: N.331 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain B: N.343, S.373 Chain E: G.44 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: N.616, T.618, Q.644 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: N.709, N.710, G.1131 Ligand excluded by PLIP NAG.29: 5 residues within 4Å: Chain B: N.717, F.718, L.922, Q.926, Q.1071 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: N.1074 Chain C: Q.895 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: V.1133, N.1134 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain B: K.558 Chain C: N.280, E.281, N.282 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain C: Y.28, N.30, F.59, N.61 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain C: N.616, T.618, Q.644, R.646 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: N.709, N.710, G.1131 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Casasnovas, J.M. et al., Nanobodies Protecting From Lethal SARS-CoV-2 Infection Target Receptor Binding Epitopes Preserved in Virus Variants Other Than Omicron. Front Immunol (2022)

Release Date

2022-06-08

Peptides

Spike glycoprotein: ABC
Camel-derived nanobody 1.29: DE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Spike glycoprotein

Camel-derived nanobody 1.29

Related Entries With Identical Sequence