SMTL ID : 7a25.1

Cryo-EM structure of the SARS-CoV-2 spike protein bound to neutralizing sybodies (Sb23)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

9 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: 2 residues within 4Å: Chain B: Y.28, N.61 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain B: C.15, V.16, N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain B: N.122, T.124, N.125, V.127, E.154, V.171 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: 6 residues within 4Å: Chain C: N.122, A.123, T.124, V.127, E.154, V.171 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain C: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain A: C.15, V.16, N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 7 residues within 4Å: Chain A: N.122, A.123, T.124, N.125, V.127, E.154, V.171 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain A: T.108, N.234 No protein-ligand interaction detected (PLIP)

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

NAG.10: 3 residues within 4Å: Chain A: N.616, T.618, E.619 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: Y.28, N.30, N.61 Ligand excluded by PLIP NAG.12: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: E.281, N.282 Chain C: K.558 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain A: N.331, P.579, Q.580, L.582 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: N.709, G.1131 Chain B: D.796 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: N.717, L.922, Q.1071 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: A.706, N.1074 Chain B: Q.895 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: N.1098, G.1099, F.1103 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain A: N.1134 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain A: N.148, N.149, S.151, M.153 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: N.164, N.165 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain A: F.342, N.343, L.368, F.374 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: N.709, G.1131 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain B: G.232, I.233, N.234 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: E.132, N.164, N.165 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: N.603, T.604 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: E.281, N.282 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: N.616, T.618 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: H.655, N.657 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain B: N.717, L.922, Q.926, Q.1071 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain B: N.1074, F.1075, T.1076 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain B: N.1098, T.1100, F.1103 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain B: N.1134 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain B: H.146, N.149, S.151 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain B: N.331 Ligand excluded by PLIP NAG.39: 5 residues within 4Å: Chain B: F.338, G.339, F.342, N.343, L.368 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain C: N.331 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain C: E.132, N.164, N.165 Ligand excluded by PLIP NAG.42: 5 residues within 4Å: Chain C: F.338, G.339, N.343, V.367, S.371 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain C: N.61 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain B: K.558 Chain C: E.281, N.282 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain C: N.616, T.618 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain C: H.655, N.657 Ligand excluded by PLIP NAG.49: 4 residues within 4Å: Chain A: D.796 Chain C: N.709, N.710, G.1131 Ligand excluded by PLIP NAG.50: 4 residues within 4Å: Chain C: N.717, L.922, Q.926, Q.1071 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain C: A.706, N.1074 Ligand excluded by PLIP NAG.52: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.53: 1 residues within 4Å: Chain C: N.1134 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain C: N.149, S.151 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Custodio, T.F. et al., Selection, biophysical and structural analysis of synthetic nanobodies that effectively neutralize SARS-CoV-2. Nat Commun (2020)

Release Date

2020-11-25

Peptides

Spike glycoprotein: ABC
Sybody 23: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Spike glycoprotein

Sybody 23

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