SMTL ID : 8h11.1

Structure of SARS-CoV-1 Spike Protein with Engineered x1 Disulfide (S370C and D967C), Closed Conformation

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

1 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: 7 residues within 4Å: Chain A: S.95, T.96, N.217 Chain B: R.434, H.435, K.437, R.439 No protein-ligand interaction detected (PLIP)

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

NAG.2: 2 residues within 4Å: Chain A: Q.22, N.55 Ligand excluded by PLIP NAG.3: 3 residues within 4Å: Chain A: R.1045, N.1070, F.1075 Ligand excluded by PLIP NAG.4: 3 residues within 4Å: Chain A: N.109, N.112, V.114 Ligand excluded by PLIP NAG.5: 3 residues within 4Å: Chain A: F.147, N.148 Chain B: Y.328 Ligand excluded by PLIP NAG.6: 2 residues within 4Å: Chain A: E.258, N.259 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain A: N.308, K.556 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain A: N.592, T.594 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain A: N.681, I.1102, G.1103 Ligand excluded by PLIP NAG.10: 1 residues within 4Å: Chain A: N.689 Ligand excluded by PLIP NAG.11: 4 residues within 4Å: Chain A: Y.768, N.773, S.775, Q.776 Ligand excluded by PLIP NAG.12: 1 residues within 4Å: Chain A: N.1046 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain A: N.1106 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain B: Q.22, N.55 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain B: N.1070, F.1075 Ligand excluded by PLIP NAG.16: 4 residues within 4Å: Chain B: N.109, N.112, V.114, I.154 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain B: F.147, N.148 Chain C: Y.328, I.445 Ligand excluded by PLIP NAG.18: 6 residues within 4Å: Chain B: S.95, N.217 Chain C: R.434, K.437, L.438, R.439 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain B: D.257, E.258, N.259 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain B: N.308, K.556 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain A: L.821, C.823 Chain B: N.592, T.594 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain B: N.681, I.1102, G.1103 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: N.689, Q.894 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain B: Y.768, N.773, S.775, Q.776 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: Q.867 Chain B: T.683, N.1046 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain B: N.1106 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain C: Q.22, N.55 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain C: R.1045, N.1070, F.1075 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain C: N.109, N.112, V.114 Ligand excluded by PLIP NAG.30: 6 residues within 4Å: Chain A: R.434, K.437, L.438, R.439 Chain C: S.95, N.217 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain A: R.534 Chain C: D.257, E.258, N.259 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain C: P.307, N.308, P.555, K.556 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: N.592, T.594 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain C: N.681, I.1102, G.1103 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain C: N.689, Q.894, Q.1043 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain C: Y.768, N.773, S.775, Q.776 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain B: Q.867 Chain C: E.1044, N.1046 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain C: N.1106 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, X. et al., Disulfide stabilization reveals conserved dynamic features between SARS-CoV-1 and SARS-CoV-2 spikes. Life Sci Alliance (2023)

Release Date

2022-11-09

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

C
C

Spike glycoprotein

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