SMTL ID : 7r4r.1

The SARS-CoV-2 spike in complex with the 1.10 neutralizing nanobody

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-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: 7 residues within 4Å: Chain A: C.15, V.16, N.17, L.18, T.19, R.21, N.137 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.19 Hydrogen bonds: A:N.17, A:N.17 NAG-NAG.2: 6 residues within 4Å: Chain B: Q.14, C.15, V.16, N.17, C.136, 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, K.129, V.171, P.174 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: 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: 4 residues within 4Å: Chain A: Y.144, H.146, M.153, S.155 Ligand excluded by PLIP NAG.7: 3 residues within 4Å: Chain A: Q.115, N.164, N.165 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain A: N.331, Q.580, T.581 Ligand excluded by PLIP NAG.9: 7 residues within 4Å: Chain A: G.339, N.343, V.367, S.371, A.372, S.373, F.374 Ligand excluded by PLIP NAG.10: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: N.616, T.618, Q.644 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: N.709, N.710, I.1130 Ligand excluded by PLIP NAG.15: 5 residues within 4Å: Chain A: T.716, N.717, L.922, Q.1071, F.1109 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: A.706, N.1074 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: N.1098, H.1101, F.1103 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: V.1133, N.1134 Ligand excluded by PLIP NAG.19: 8 residues within 4Å: Chain B: N.122, A.123, T.124, N.125, V.127, K.129, E.154, F.157 Ligand excluded by PLIP NAG.20: 5 residues within 4Å: Chain B: Y.144, H.146, S.151, W.152, M.153 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain B: K.113, N.165 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: E.281, N.282 Ligand excluded by PLIP NAG.23: 8 residues within 4Å: Chain B: R.328, F.329, P.330, F.543, N.544, Q.564, V.576, R.577 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain B: F.342, N.343, W.436 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain B: Y.28, N.61, V.62, T.63 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain B: D.614, V.615, N.616, Q.644 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain B: S.708, N.709, N.710, I.1130 Ligand excluded by PLIP NAG.28: 5 residues within 4Å: Chain B: T.716, N.717, L.922, Q.1071, F.1109 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: A.706, K.1073, N.1074 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: V.1133, N.1134 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain C: E.281, N.282 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: N.331, T.581 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.61, V.62, T.63 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain C: N.616, C.617, T.618, Q.644 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain A: D.796, G.798 Chain C: N.709, I.1130 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 1.10: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Spike glycoprotein

Camel-derived nanobody 1.10

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