SMTL ID : 6xf6.1

Cryo-EM structure of a biotinylated SARS-CoV-2 spike probe in the prefusion state (1 RBD up)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

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: 5 residues within 4Å: Chain A: N.223, T.225 Chain C: S.448, K.451, E.454 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.448, C:S.448 NAG-NAG.2: 5 residues within 4Å: Chain A: N.706, T.708, L.911, Q.915, Q.1060 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.790, S.792, Q.793 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.1087, T.1089, H.1090, F.1092 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain A: I.1121, N.1123 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain B: N.790, S.792, Q.793 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain B: N.1087, T.1089, H.1090, F.1092 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain B: I.1121, V.1122, N.1123 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain C: N.706, L.911, Q.915, Q.1060 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain C: N.790, S.792, Q.793 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain C: N.1087, T.1089, H.1090, F.1092 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain C: I.1121, N.1123 No protein-ligand interaction detected (PLIP)

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

NAG.13: 3 residues within 4Å: Chain A: Y.17, T.18, N.50 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: N.111, T.113, V.116 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: N.269, E.270, N.271 Ligand excluded by PLIP NAG.16: 4 residues within 4Å: Chain A: P.319, N.320, P.568, Q.569 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain A: N.592 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: N.605, T.607 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: H.644, V.645, N.646 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: N.698, G.1120 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain A: A.695, E.1061, K.1062, N.1063 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain A: G.328, F.331, N.332, V.356 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: Y.17, N.50 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain B: N.111, A.112, V.116, K.118 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain B: T.97, N.223, T.225 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain B: N.269, E.270, N.271 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: N.320, P.568, Q.569 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: F.327, F.331, N.332 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.592 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: N.605, T.607, E.608 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: H.644, N.646 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain B: N.698 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain B: N.706, L.911, Q.915, Q.1060 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain B: E.1061, N.1063 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain B: E.121, N.154 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: Y.17, N.50 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain C: N.111, T.113, V.116 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: G.221, N.223 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: N.269, N.271 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: N.320, Q.569 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: G.328, N.332 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain C: N.592 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: N.605, T.607 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: H.644, N.646 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain C: N.698, I.1119, G.1120 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain C: E.1061, N.1063 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain C: N.154 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, T. et al., Structure-Based Design with Tag-Based Purification and In-Process Biotinylation Enable Streamlined Development of SARS-CoV-2 Spike Molecular Probes. SSRN (2020)

Release Date

2020-09-02

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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