SMTL ID : 6zxn.1

Cryo-EM structure of the SARS-CoV-2 spike protein bound to neutralizing nanobodies (Ty1)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

12 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: 4 residues within 4Å: Chain A: P.26, Y.28, T.29, N.61 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.28 NAG-NAG.2: 5 residues within 4Å: Chain A: Q.14, C.15, V.16, N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 8 residues within 4Å: Chain A: 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: 4 residues within 4Å: Chain A: T.108, N.234, T.236 Chain C: S.469 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain B: P.26, Y.28, N.61 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.28 NAG-NAG.6: 4 residues within 4Å: Chain B: C.15, V.16, N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 8 residues within 4Å: Chain B: N.122, A.123, T.124, N.125, V.127, E.154, V.171, P.174 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain B: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain C: P.26, Y.28, N.30, N.61 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.28 NAG-NAG.10: 5 residues within 4Å: Chain C: C.15, V.16, N.17, C.136, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 7 residues within 4Å: Chain C: N.122, A.123, T.124, N.125, V.127, E.154, V.171 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 5 residues within 4Å: Chain B: K.462, E.465 Chain C: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP)

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

NAG.13: 4 residues within 4Å: Chain A: N.280, E.281, N.282 Chain C: K.558 Ligand excluded by PLIP NAG.14: 5 residues within 4Å: Chain A: N.331, P.579, Q.580, T.581, L.582 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: N.603, T.604 Ligand excluded by PLIP NAG.16: 4 residues within 4Å: Chain A: N.616, T.618, Q.644, R.646 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.18: 5 residues within 4Å: Chain A: N.709, N.710, I.1130, G.1131 Chain B: D.796 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain A: T.716, N.717, L.922, Q.1071 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain A: A.706, A.713, N.1074 Chain B: Q.895 Ligand excluded by PLIP NAG.21: 5 residues within 4Å: Chain A: N.1098, G.1099, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain A: N.1134 Ligand excluded by PLIP NAG.23: 5 residues within 4Å: Chain A: H.146, N.148, N.149, S.151, M.153 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain A: N.164, N.165 Ligand excluded by PLIP NAG.25: 5 residues within 4Å: Chain A: G.339, F.342, N.343, L.368, F.374 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: E.281, N.282 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: T.307, N.603 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain B: N.616, T.618, Q.644, R.646 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: H.655, V.656, N.657 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain B: N.717, L.922, Q.926, Q.1071 Ligand excluded by PLIP NAG.31: 5 residues within 4Å: Chain B: N.1074, F.1075, T.1076, S.1097, G.1099 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: V.1133, N.1134 Ligand excluded by PLIP NAG.34: 5 residues within 4Å: Chain B: H.146, N.148, N.149, S.151, M.153 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain B: N.164, N.165 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain B: N.331 Ligand excluded by PLIP NAG.37: 5 residues within 4Å: Chain B: F.338, G.339, F.342, N.343, L.368 Ligand excluded by PLIP NAG.38: 5 residues within 4Å: Chain B: N.709, N.710, I.1130, G.1131 Chain C: D.796 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain B: K.558 Chain C: N.280, E.281, N.282 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain C: N.616, T.618, Q.644, R.646 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain C: H.655, N.657 Ligand excluded by PLIP NAG.43: 6 residues within 4Å: Chain A: D.796 Chain C: N.709, N.710, P.1079, I.1130, G.1131 Ligand excluded by PLIP NAG.44: 5 residues within 4Å: Chain C: T.716, N.717, L.922, Q.926, Q.1071 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain A: Q.895 Chain C: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.46: 5 residues within 4Å: Chain C: N.1098, G.1099, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain C: N.1134 Ligand excluded by PLIP NAG.48: 4 residues within 4Å: Chain C: H.146, N.148, N.149, S.151 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain C: N.164, N.165 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain C: N.331 Ligand excluded by PLIP NAG.51: 6 residues within 4Å: Chain C: F.338, G.339, F.342, N.343, L.368, F.374 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hanke, L. et al., An alpaca nanobody neutralizes SARS-CoV-2 by blocking receptor interaction. Nat Commun (2020)

Release Date

2020-09-23

Peptides

Spike glycoprotein: ABC
Nanobody Ty1: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Spike glycoprotein

Nanobody Ty1

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