SMTL ID : 8cyb.1

SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 1-8

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-mer

Ligands

4 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: 3 residues within 4Å: Chain A: N.331, Q.580, L.582 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain A: N.1134 Ligands: AH2.34 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 2 residues within 4Å: Chain C: N.331, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain C: N.616, T.618, Q.644 No protein-ligand interaction detected (PLIP)

7 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.2: 3 residues within 4Å: Chain A: N.709, N.710, G.1131 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.3: 5 residues within 4Å: Chain A: N.717, L.922, N.925, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.922 NAG-NAG-BMA-MAN-MAN.4: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.6: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.1101 NAG-NAG-BMA-MAN-MAN.9: 4 residues within 4Å: Chain B: N.1098, G.1099, H.1101, F.1103 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.1101 NAG-NAG-BMA-MAN-MAN.11: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.18: 4 residues within 4Å: Chain C: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP)

1 x NAG- FUC- GAL- FUC- NAG- BMA: alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-alpha-L-fucopyranose-(1-6)-[beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-FUC-GAL-FUC-NAG-BMA.5: 5 residues within 4Å: Chain A: A.706, E.1072, K.1073, N.1074 Chain C: Q.895 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.1074

7 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.8: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 4 residues within 4Å: Chain B: N.717, L.922, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.922 NAG-NAG-BMA.13: 3 residues within 4Å: Chain B: N.709, N.710, G.1131 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 3 residues within 4Å: Chain B: N.331, I.332, T.333 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.17: 3 residues within 4Å: Chain C: N.709, I.1130, G.1131 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.21: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.1101 NAG-NAG-BMA.22: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- FUC: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-FUC.10: 4 residues within 4Å: Chain A: Q.895 Chain B: A.706, S.711, N.1074 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.19: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP)

1 x NAG- FUC- NAG: alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-FUC-NAG.20: 3 residues within 4Å: Chain C: A.706, S.711, N.1074 No protein-ligand interaction detected (PLIP)

32 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.23: 6 residues within 4Å: Chain A: C.15, V.16, N.17, C.136, N.137, D.138 Ligand excluded by PLIP NAG.24: 5 residues within 4Å: Chain A: Y.28, F.59, S.60, N.61, P.631 Ligand excluded by PLIP NAG.25: 5 residues within 4Å: Chain A: N.122, N.125, E.154, F.157, V.171 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain A: H.146, N.148, N.149 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain A: Q.115, E.132, N.165 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain A: G.232, I.233, N.234 Chain B: H.519 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain A: N.280, E.281, N.282 Chain B: K.558 Ligand excluded by PLIP NAG.30: 5 residues within 4Å: Chain A: F.342, N.343, V.367, S.371, F.374 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain A: N.603, T.604 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain A: N.616, T.618 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain A: V.656, N.657 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 B: N.616, T.618, Q.644 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain B: T.307, N.603 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain B: N.343 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain B: N.282 Chain C: K.558 Ligand excluded by PLIP NAG.40: 5 residues within 4Å: Chain B: T.108, N.234, T.236 Chain C: E.465, R.466 Ligand excluded by PLIP NAG.41: 5 residues within 4Å: Chain B: Q.115, E.132, N.164, N.165, T.167 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain B: H.146, N.148, N.149 Ligand excluded by PLIP NAG.43: 6 residues within 4Å: Chain B: N.122, N.125, V.127, K.129, F.157, Y.160 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain B: Y.28, F.59, N.61, T.630 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain B: C.15, V.16, N.17, N.137 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain C: C.15, V.16, N.17, N.137 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain C: Y.28, N.61, T.630 Ligand excluded by PLIP NAG.48: 5 residues within 4Å: Chain C: N.122, N.125, V.127, E.154, F.157 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain C: H.146, N.148, N.149 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain C: Q.115, E.132, N.165 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain C: T.108, T.114, N.234 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain A: K.558 Chain C: E.281, N.282 Ligand excluded by PLIP NAG.53: 4 residues within 4Å: Chain C: F.342, N.343, V.367, S.371 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain C: N.603, T.604 Ligand excluded by PLIP NAG.55: 2 residues within 4Å: Chain C: V.656, N.657 Ligand excluded by PLIP

1 x AH2: 1-deoxy-alpha-D-mannopyranose(Non-functional Binders)

AH2.34: 1 residues within 4Å: Ligands: NAG-NAG.7 No protein-ligand interaction detected (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 1-8: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Spike glycoprotein

pan-sarbecovirus nanobody 1-8

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