SMTL ID : 8h12.1

Structure of SARS-CoV-1 Spike Protein with Engineered x2 Disulfide (G400C and V969C), Locked-2 Conformation

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

3 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.91, N.213 Chain C: R.430, H.431, K.433, R.435, E.438 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 7 residues within 4Å: Chain A: R.430, H.431, K.433, R.435, E.438 Chain B: S.91, N.213 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 7 residues within 4Å: Chain B: R.430, H.431, K.433, R.435, E.438 Chain C: S.91, N.213 No protein-ligand interaction detected (PLIP)

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

NAG.4: 4 residues within 4Å: Chain A: Q.18, T.20, Y.49, N.51 Ligand excluded by PLIP NAG.5: 2 residues within 4Å: Chain A: N.1066, F.1071 Ligand excluded by PLIP NAG.6: 2 residues within 4Å: Chain A: N.95, E.117 Ligand excluded by PLIP NAG.7: 4 residues within 4Å: Chain A: N.105, T.107, N.108, V.110 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain A: N.144 Chain C: A.325, I.441 Ligand excluded by PLIP NAG.9: 4 residues within 4Å: Chain A: D.253, E.254, N.255 Chain C: R.530 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: N.304, K.552 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: N.343 Chain C: Y.428, Y.461 Ligand excluded by PLIP NAG.12: 1 residues within 4Å: Chain A: N.588 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: N.677, G.1099 Ligand excluded by PLIP NAG.14: 1 residues within 4Å: Chain A: N.685 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: Y.764, N.769, S.771 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: E.1040, N.1042 Chain B: Q.863 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain B: Q.18, T.20, Y.49, N.51 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain B: R.1041, N.1066, G.1067, F.1071 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain B: N.95, E.117 Ligand excluded by PLIP NAG.20: 6 residues within 4Å: Chain B: N.105, S.106, T.107, N.108, V.110, I.150 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain A: A.325, I.441 Chain B: N.144 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain A: R.530 Chain B: D.253, E.254, N.255 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: N.304, K.552 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain A: Y.428, Y.461 Chain B: N.343 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: N.588, D.591 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: N.677, G.1099 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain B: N.685 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain B: Y.764, N.769, S.771, Q.772 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: E.1040, N.1042 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain C: Q.18, T.20, Y.49, N.51 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain C: N.1066, T.1068, F.1071, P.1080 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain C: N.95, E.117 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain C: N.105, T.107, N.108, V.110 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain B: A.325, I.441 Chain C: N.144 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain C: D.253, E.254, N.255 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: N.304, K.552 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain B: Y.428, Y.461 Chain C: N.343 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain C: N.588 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: N.677, G.1099 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: N.685, Q.890 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain C: Y.764, N.769, S.771, Q.772 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain A: Q.863 Chain C: E.1040, N.1042 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
A

B
B

C
C

Spike glycoprotein

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