SMTL ID : 6xf5.1

Cryo-EM structure of a biotinylated SARS-CoV-2 spike probe in the prefusion state (RBDs down)

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: 4 residues within 4Å: Chain A: N.706, L.911, Q.915, Q.1060 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.790, S.792, Q.793 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.1087, T.1089, H.1090, F.1092 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain A: N.1123 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain B: N.706, L.911, Q.915, Q.1060 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: 1 residues within 4Å: Chain B: 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: 1 residues within 4Å: Chain C: N.1123 No protein-ligand interaction detected (PLIP)

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

NAG.13: 1 residues within 4Å: Chain A: N.50 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain A: N.111, N.114, V.116, K.118 Ligand excluded by PLIP NAG.15: 5 residues within 4Å: Chain A: T.97, N.223, T.225, R.226 Chain C: E.454 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: N.269, E.270, N.271 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain A: P.319, N.320, P.568, Q.569 Ligand excluded by PLIP NAG.18: 5 residues within 4Å: Chain A: F.327, G.328, F.331, N.332, V.356 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain A: N.592 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: N.605, Q.633 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: H.644, N.646 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain A: N.698, G.1120 Chain B: D.785 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain A: A.695, E.1061, K.1062, N.1063 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain A: E.121, N.154 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain B: N.50 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain B: N.111, N.114, V.116, K.118 Ligand excluded by PLIP NAG.27: 6 residues within 4Å: Chain A: K.451, E.454 Chain B: T.97, N.223, T.225, R.226 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain A: K.547 Chain B: N.269, E.270, N.271 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain B: P.319, N.320, P.568, Q.569 Ligand excluded by PLIP NAG.30: 5 residues within 4Å: Chain B: F.327, G.328, F.331, N.332, V.356 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain B: N.592 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: N.605, Q.633 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: H.644, N.646 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain B: N.698, I.1119, G.1120 Chain C: D.785 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain B: A.695, E.1061, K.1062, N.1063 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain B: E.121, N.154 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain C: N.50 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain C: N.111, N.114, V.116, K.118 Ligand excluded by PLIP NAG.39: 6 residues within 4Å: Chain B: K.451, E.454 Chain C: T.97, N.223, T.225, R.226 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain C: N.269, E.270, N.271 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain C: P.319, N.320, P.568, Q.569 Ligand excluded by PLIP NAG.42: 5 residues within 4Å: Chain C: F.327, G.328, F.331, N.332, V.356 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain C: N.592 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: N.605, Q.633 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain C: H.644, N.646 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain A: D.785 Chain C: N.698, I.1119, G.1120 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain C: A.695, E.1061, K.1062, N.1063 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain C: E.121, 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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