SMTL ID : 8h14.1

Structure of SARS-CoV-1 Spike Protein with Engineered x3 Disulfide (D414C and V969C), Locked-1 Conformation

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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

NAG.1: 1 residues within 4Å: Chain A: N.55 Ligand excluded by PLIP NAG.2: 1 residues within 4Å: Chain A: N.1070 Ligand excluded by PLIP NAG.3: 2 residues within 4Å: Chain A: N.99, E.121 Ligand excluded by PLIP NAG.4: 4 residues within 4Å: Chain A: N.109, S.110, T.111, N.112 Ligand excluded by PLIP NAG.5: 4 residues within 4Å: Chain A: F.147, N.148 Chain C: A.329, I.445 Ligand excluded by PLIP NAG.6: 2 residues within 4Å: Chain A: N.217 Chain C: E.442 Ligand excluded by PLIP NAG.7: 4 residues within 4Å: Chain A: D.257, E.258, N.259 Chain C: R.534 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain A: N.308, K.556 Ligand excluded by PLIP NAG.9: 1 residues within 4Å: Chain A: N.320 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain A: N.347 Chain C: Y.432, Y.465 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: N.592 Chain B: M.806 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: N.689, Q.894 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain A: Y.768, N.773, S.775, Q.776 Ligand excluded by PLIP NAG.14: 1 residues within 4Å: Chain A: N.1106 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain B: N.55 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain B: N.1070 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain B: N.99, E.121 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain B: N.109, S.110, T.111, N.112 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain A: A.329, I.445 Chain B: F.147, N.148 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: E.442 Chain B: N.217 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain A: R.534 Chain B: D.257, E.258, N.259 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: N.308, K.556 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain B: N.320 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: Y.432, Y.465 Chain B: N.347 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: N.592 Chain C: M.806 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: N.689, Q.894 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain B: Y.768, N.773, S.775, Q.776 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.1106 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain C: N.55 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain C: N.1070 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain C: N.99, E.121 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain C: N.109, S.110, T.111, N.112 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain B: A.329, I.445 Chain C: F.147, N.148 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain C: N.217 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain B: R.534 Chain C: D.257, E.258, N.259 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: N.308, K.556 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain C: N.320 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain B: Y.432, Y.465 Chain C: N.347 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain A: M.806 Chain C: N.592 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: N.689, Q.894 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain C: Y.768, N.773, S.775, Q.776 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain C: N.1106 Ligand excluded by PLIP

3 x EIC: LINOLEIC ACID(Non-covalent)

EIC.15: 13 residues within 4Å: Chain A: R.385, T.392, G.393 Chain B: C.313, P.314, F.315, V.318, Y.342, L.345, F.351, F.354, F.369, L.411 14 PLIP interactions: 12 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.315, B:F.315, B:V.318, B:Y.342, B:Y.342, B:L.345, B:F.351, B:F.351, B:F.354, B:F.369, B:F.369, B:L.411 Hydrogen bonds: A:T.392 Salt bridges: A:R.385 EIC.30: 13 residues within 4Å: Chain B: R.385, T.392, G.393 Chain C: C.313, P.314, F.315, V.318, Y.342, L.345, F.351, F.354, F.369, L.411 14 PLIP interactions: 12 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:F.315, C:F.315, C:V.318, C:Y.342, C:Y.342, C:L.345, C:F.351, C:F.351, C:F.354, C:F.369, C:F.369, C:L.411 Hydrogen bonds: B:T.392 Salt bridges: B:R.385 EIC.31: 13 residues within 4Å: Chain A: C.313, P.314, F.315, V.318, Y.342, L.345, F.351, F.354, F.369, L.411 Chain C: R.385, T.392, G.393 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:F.315, A:F.315, A:V.318, A:Y.342, A:Y.342, A:L.345, A:F.351, A:F.351, A:F.354, A:F.369, A:F.369, A:L.411 Hydrogen bonds: C:T.392 Salt bridges: C:R.385

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

2022-10-19

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein