SMTL ID : 8cya.1

SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 2-67

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

14 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.1: 3 residues within 4Å: Chain A: I.1132, V.1133, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 5 residues within 4Å: Chain A: N.1098, G.1099, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 6 residues within 4Å: Chain A: N.717, T.719, L.922, N.925, Q.926, Q.1071 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.922, A:Q.926 NAG-NAG-BMA.9: 8 residues within 4Å: Chain B: T.716, N.717, F.718, T.719, L.922, N.925, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.922 NAG-NAG-BMA.11: 5 residues within 4Å: Chain B: N.1098, G.1099, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 3 residues within 4Å: Chain B: I.1132, V.1133, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 4 residues within 4Å: Chain B: K.558, L.560 Chain C: E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 4 residues within 4Å: Chain C: N.331, Q.580, T.581, L.582 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 5 residues within 4Å: Chain A: D.796 Chain C: N.709, N.710, I.1130, G.1131 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.16: 7 residues within 4Å: Chain C: N.717, F.718, T.719, L.922, N.925, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.922 NAG-NAG-BMA.17: 4 residues within 4Å: Chain C: K.795, N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.19: 5 residues within 4Å: Chain C: N.1098, G.1099, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.20: 3 residues within 4Å: Chain C: I.1132, V.1133, N.1134 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.5: 5 residues within 4Å: Chain A: N.709, N.710, I.1130, G.1131 Chain B: D.796 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain A: N.331, P.579, Q.580, T.581, L.582 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain B: N.331, I.332, Q.580, T.581 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain B: N.709, N.710, I.1130, G.1131 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-FUC.10: 8 residues within 4Å: Chain B: A.706, N.1074, F.1075, T.1076, S.1097, N.1098, G.1099 Chain C: Q.895 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.1074 NAG-NAG-FUC.18: 10 residues within 4Å: Chain A: Q.895 Chain C: S.704, V.705, A.706, Y.707, S.708, S.711, N.1074, F.1075, T.1076 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:A.706

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

NAG.21: 4 residues within 4Å: Chain A: A.706, N.1074, F.1075, T.1076 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain A: E.654, H.655, V.656, N.657 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: N.616, T.618, Q.644 Ligand excluded by PLIP NAG.24: 5 residues within 4Å: Chain A: E.309, K.310, G.601, N.603, T.604 Ligand excluded by PLIP NAG.25: 8 residues within 4Å: Chain A: N.343, S.371, S.373, W.436, N.437, S.438, N.440, L.441 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain A: E.281, N.282 Chain C: K.558 Ligand excluded by PLIP NAG.27: 6 residues within 4Å: Chain A: T.108, G.232, N.234, T.236 Chain C: L.518, H.519 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain A: Q.115, E.132, N.165, T.167 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain A: H.146, N.148, N.149, M.153 Ligand excluded by PLIP NAG.30: 9 residues within 4Å: Chain A: V.120, N.121, N.122, A.123, T.124, N.125, V.126, V.127, F.175 Ligand excluded by PLIP NAG.31: 6 residues within 4Å: Chain A: Y.28, T.29, N.30, N.61, T.630, P.631 Ligand excluded by PLIP NAG.32: 6 residues within 4Å: Chain A: C.15, V.16, N.17, C.136, N.137, D.138 Ligand excluded by PLIP NAG.33: 6 residues within 4Å: Chain B: C.15, V.16, N.17, C.136, N.137, D.138 Ligand excluded by PLIP NAG.34: 9 residues within 4Å: Chain B: Y.28, T.29, N.30, S.31, F.59, N.61, V.62, T.630, P.631 Ligand excluded by PLIP NAG.35: 7 residues within 4Å: Chain B: N.122, T.124, N.125, V.127, K.129, F.157, V.171 Ligand excluded by PLIP NAG.36: 5 residues within 4Å: Chain B: Q.115, E.132, N.165, T.167 Ligands: NAG.37 Ligand excluded by PLIP NAG.37: 5 residues within 4Å: Chain A: H.519 Chain B: G.232, I.233, N.234 Ligands: NAG.36 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain A: K.558 Chain B: E.281, N.282 Ligand excluded by PLIP NAG.39: 11 residues within 4Å: Chain B: G.339, F.342, N.343, Y.365, V.367, L.368, Y.369, N.370, S.371, A.372, F.374 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain B: N.603, T.604 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain B: N.616, T.618, Q.644 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain B: K.795, N.801, S.803, Q.804 Ligand excluded by PLIP NAG.44: 5 residues within 4Å: Chain C: C.15, V.16, N.17, C.136, N.137 Ligand excluded by PLIP NAG.45: 5 residues within 4Å: Chain C: N.30, F.59, N.61, T.630, P.631 Ligand excluded by PLIP NAG.46: 6 residues within 4Å: Chain C: N.122, T.124, N.125, V.127, E.169, V.171 Ligand excluded by PLIP NAG.47: 6 residues within 4Å: Chain C: H.146, N.148, N.149, S.151, W.152, M.153 Ligand excluded by PLIP NAG.48: 4 residues within 4Å: Chain B: H.519 Chain C: T.108, T.114, N.234 Ligand excluded by PLIP NAG.49: 11 residues within 4Å: Chain C: F.342, N.343, A.344, F.347, S.371, S.373, W.436, S.438, N.440, L.441, R.509 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.51: 4 residues within 4Å: Chain C: N.616, C.617, T.618, Q.644 Ligand excluded by PLIP NAG.52: 1 residues within 4Å: Chain C: N.657 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 2-67: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

C
C

D
D

E
E

F
F

Spike glycoprotein

pan-sarbecovirus nanobody 2-67

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