SMTL ID : 8h0x.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

3 x EIC: LINOLEIC ACID(Non-covalent)

EIC.1: 14 residues within 4Å: Chain A: C.313, P.314, F.315, V.318, A.340, Y.342, F.354, L.364, F.369, V.372, L.411 Chain C: R.385, T.392, G.393 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:F.315, A:F.315, A:V.318, A:A.340, A:Y.342, A:L.364, A:L.364, A:F.369, A:F.369, A:V.372, A:L.411 Salt bridges: C:R.385 EIC.17: 14 residues within 4Å: Chain A: R.385, T.392, G.393 Chain B: C.313, P.314, F.315, V.318, A.340, Y.342, F.354, L.364, F.369, V.372, L.411 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.315, B:F.315, B:V.318, B:A.340, B:Y.342, B:L.364, B:L.364, B:F.369, B:F.369, B:V.372, B:L.411 Salt bridges: A:R.385 EIC.33: 13 residues within 4Å: Chain B: R.385, T.392 Chain C: C.313, P.314, F.315, V.318, A.340, Y.342, F.354, L.364, F.369, V.372, L.411 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:F.315, C:F.315, C:V.318, C:A.340, C:Y.342, C:L.364, C:L.364, C:F.369, C:F.369, C:V.372, C:L.411 Salt bridges: B:R.385

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

NAG.2: 1 residues within 4Å: Chain A: N.55 Ligand excluded by PLIP NAG.3: 4 residues within 4Å: Chain A: R.1045, N.1070, T.1072, F.1075 Ligand excluded by PLIP NAG.4: 4 residues within 4Å: Chain A: N.99, E.121, F.147 Ligands: NAG.6 Ligand excluded by PLIP NAG.5: 5 residues within 4Å: Chain A: N.109, T.111, N.112, V.114, I.154 Ligand excluded by PLIP NAG.6: 5 residues within 4Å: Chain A: F.147, N.148 Chain C: A.329, I.445 Ligands: NAG.4 Ligand excluded by PLIP NAG.7: 4 residues within 4Å: Chain A: S.95, T.96, N.217 Chain C: R.439 Ligand excluded by PLIP NAG.8: 4 residues within 4Å: Chain A: D.257, E.258, N.259 Chain C: R.534 Ligand excluded by PLIP NAG.9: 2 residues within 4Å: Chain A: N.308, K.556 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain A: N.320, S.348, T.349 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: N.347 Chain C: Y.432, Y.465 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: N.592 Chain B: M.806 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: N.689, Q.1043 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain A: Y.768, N.773, S.775, Q.776 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain A: N.1106 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain B: N.55 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain B: R.1045, N.1070, T.1072, F.1075 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain B: N.99, E.121, F.147 Ligands: NAG.22 Ligand excluded by PLIP NAG.21: 5 residues within 4Å: Chain B: N.109, T.111, N.112, V.114, I.154 Ligand excluded by PLIP NAG.22: 5 residues within 4Å: Chain A: A.329, I.445 Chain B: F.147, N.148 Ligands: NAG.20 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain A: R.439 Chain B: S.95, T.96, N.217 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain A: R.534 Chain B: D.257, E.258, N.259 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: N.308, K.556 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain B: N.320, S.348, T.349 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain A: Y.432, Y.465 Chain B: N.347 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: N.592 Chain C: M.806 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: N.689, Q.1043 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain B: Y.768, N.773, S.775, Q.776 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain B: N.1106 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain C: N.55 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain C: R.1045, N.1070, T.1072, F.1075 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain C: N.99, E.121, F.147 Ligands: NAG.38 Ligand excluded by PLIP NAG.37: 5 residues within 4Å: Chain C: N.109, T.111, N.112, V.114, I.154 Ligand excluded by PLIP NAG.38: 6 residues within 4Å: Chain B: Y.328, A.329, I.445 Chain C: F.147, N.148 Ligands: NAG.36 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain B: R.439 Chain C: S.95, T.96, N.217 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain B: R.534 Chain C: D.257, E.258, N.259 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: N.308, K.556 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: N.320, S.348, T.349 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain B: Y.432, Y.465 Chain C: N.347 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain A: M.806 Chain C: N.592 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain C: N.689, Q.1043 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain C: Y.768, N.773, S.775, Q.776 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain C: N.1106 Ligand excluded by PLIP

3 x BLA: BILIVERDINE IX ALPHA(Non-covalent)

BLA.16: 11 residues within 4Å: Chain A: N.86, V.88, R.89, W.91, N.108, V.113, R.173, F.175, K.188, I.209, F.210 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.91, A:V.113, A:K.188, A:I.209, A:F.210 Hydrogen bonds: A:N.108, A:K.188, A:K.188 pi-Cation interactions: A:R.173, A:K.188 BLA.32: 11 residues within 4Å: Chain B: N.86, V.88, R.89, W.91, N.108, V.113, R.173, F.175, K.188, I.209, F.210 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:W.91, B:V.113, B:K.188, B:I.209, B:F.210 Hydrogen bonds: B:N.108, B:K.188, B:K.188 pi-Cation interactions: B:R.173, B:K.188 BLA.48: 11 residues within 4Å: Chain C: N.86, V.88, R.89, W.91, N.108, V.113, R.173, F.175, K.188, I.209, F.210 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:W.91, C:V.113, C:K.188, C:I.209, C:F.210 Hydrogen bonds: C:N.108, C:K.188, C:K.188 pi-Cation interactions: C:R.173, C:K.188

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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