SMTL ID : 8cxn.1

SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 2-57

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

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

NAG.1: 6 residues within 4Å: Chain A: F.59, S.60, N.61, L.629, T.630, P.631 Ligand excluded by PLIP NAG.2: 3 residues within 4Å: Chain A: N.122, T.124, V.171 Ligand excluded by PLIP NAG.3: 4 residues within 4Å: Chain A: N.280, E.281, N.282 Chain B: K.558 Ligand excluded by PLIP NAG.4: 5 residues within 4Å: Chain A: N.331, P.579, Q.580, T.581, L.582 Ligand excluded by PLIP NAG.5: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NAG.6: 4 residues within 4Å: Chain A: K.310, G.601, N.603, T.604 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain A: N.616, T.618 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain A: V.656, N.657 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain A: N.709, N.710, G.1131 Ligand excluded by PLIP NAG.10: 7 residues within 4Å: Chain A: V.705, A.713, E.1072, K.1073, N.1074 Chain C: A.893, Q.895 Ligand excluded by PLIP NAG.11: 4 residues within 4Å: Chain B: Y.28, N.61, L.629, P.631 Ligand excluded by PLIP NAG.12: 1 residues within 4Å: Chain B: V.127 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain B: N.280, E.281, N.282 Chain C: K.558 Ligand excluded by PLIP NAG.14: 6 residues within 4Å: Chain B: N.331, I.332, N.334, Q.580, T.581, L.582 Ligand excluded by PLIP NAG.15: 5 residues within 4Å: Chain B: L.335, N.440, L.441, D.442, S.443 Ligand excluded by PLIP NAG.16: 5 residues within 4Å: Chain B: E.309, K.310, G.601, N.603, T.604 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain B: N.616, Q.644 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain B: H.655, V.656, N.657 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain B: N.709, N.710, I.1130, G.1131 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: Q.895 Chain B: A.706, N.1074 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain C: Y.28, N.61, P.631 Ligand excluded by PLIP NAG.22: 7 residues within 4Å: Chain C: N.122, T.124, N.125, V.127, K.129, E.154, V.171 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain C: N.280, E.281, N.282, T.284 Ligand excluded by PLIP NAG.24: 5 residues within 4Å: Chain C: N.331, Q.580, T.581, L.582 Ligands: NAG.25 Ligand excluded by PLIP NAG.25: 5 residues within 4Å: Chain C: N.331, I.332, V.367, N.370 Ligands: NAG.24 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain C: N.616, T.618 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain C: H.655, V.656, N.657 Ligand excluded by PLIP NAG.29: 5 residues within 4Å: Chain B: D.796 Chain C: N.709, N.710, I.1130, G.1131 Ligand excluded by PLIP NAG.30: 8 residues within 4Å: Chain B: L.894, Q.895 Chain C: V.705, A.706, A.713, E.1072, K.1073, N.1074 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xiang, Y. et al., Superimmunity by pan-sarbecovirus nanobodies. Cell Rep (2022)

Release Date

2022-07-06

Peptides

Spike glycoprotein: ABC
pan-sarbecovirus nanobody 2-57: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
F

F
E

Spike glycoprotein

pan-sarbecovirus nanobody 2-57

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