SMTL ID : 7r4i.1

The SARS-CoV-2 spike in complex with the 2.15 neutralizing nanobody

Coordinates

PDB Format

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)(Post Translational Modification)

NAG-NAG.1: 3 residues within 4Å: Chain A: V.16, N.17, T.19 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain B: C.15, V.16, N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 8 residues within 4Å: Chain C: N.122, A.123, T.124, N.125, V.127, E.154, V.171, P.174 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain C: C.15, V.16, N.17, N.137, D.138 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain B: E.465 Chain C: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP)

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

NAG.6: 3 residues within 4Å: Chain A: H.146, N.148, M.153 Ligand excluded by PLIP NAG.7: 1 residues within 4Å: Chain A: N.165 Ligand excluded by PLIP NAG.8: 4 residues within 4Å: Chain A: N.280, E.281, N.282 Chain C: K.558 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: 3 residues within 4Å: Chain A: G.339, E.340, N.343 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, E.619, Q.644 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: V.656, N.657 Ligand excluded by PLIP NAG.15: 5 residues within 4Å: Chain A: N.709, N.710, I.1130, G.1131 Chain B: D.796 Ligand excluded by PLIP NAG.16: 4 residues within 4Å: Chain A: T.716, N.717, L.922, Q.1071 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain A: N.1074 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: 6 residues within 4Å: Chain B: N.122, A.123, T.124, N.125, E.154, V.171 Ligand excluded by PLIP NAG.21: 5 residues within 4Å: Chain B: H.146, N.148, N.149, S.151, M.153 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: N.164, N.165 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: E.281, N.282 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain B: P.330, N.331, I.332 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain B: G.339, F.342, N.343, F.374 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain B: Y.28, T.29, N.30, N.61 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: N.616, T.618, R.646 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain B: N.709, I.1130, G.1131 Chain C: D.796 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain B: N.717, L.922, Q.926, Q.1071 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: N.1074, F.1075 Ligand excluded by PLIP NAG.31: 5 residues within 4Å: Chain B: N.1098, G.1099, 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: 5 residues within 4Å: Chain B: K.557, 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, F.59, S.60, N.61 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain C: N.616, 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, I.1130, 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 2.15: DE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Spike glycoprotein

Camel-derived nanobody 2.15

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