SMTL ID : 8h0y.1

Structure of SARS-CoV-1 Spike Protein with Engineered x1 Disulfide (S370C and D967C), Locked-112 Conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

3 x EIC: LINOLEIC ACID(Non-covalent)

EIC.1: 12 residues within 4Å: Chain A: C.313, P.314, F.315, A.340, Y.342, Y.346, F.351, F.354, F.369, L.411, L.489 Chain B: G.393 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.315, A:F.315, A:A.340, A:Y.342, A:Y.342, A:F.351, A:F.354, A:F.354, A:F.369, A:L.411, A:L.489, A:L.489 EIC.19: 14 residues within 4Å: Chain B: C.313, P.314, F.315, A.340, Y.342, Y.346, F.351, F.354, F.369, V.372, L.411, L.489, V.500 Chain C: R.385 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:F.315, B:A.340, B:Y.342, B:F.354, B:F.354, B:F.369, B:V.372, B:L.411, B:L.489, B:V.500 Salt bridges: C:R.385 EIC.36: 17 residues within 4Å: Chain A: R.385, T.392, G.393 Chain C: C.313, P.314, F.315, V.318, A.340, Y.346, F.351, F.354, F.369, V.372, L.411, L.489, F.491, V.500 13 PLIP interactions: 11 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:F.315, C:V.318, C:A.340, C:F.351, C:F.354, C:F.369, C:V.372, C:L.411, C:L.489, C:F.491, C:V.500 Hydrogen bonds: A:R.385, A:T.392

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

NAG.2: 2 residues within 4Å: Chain A: N.1046 Chain C: Q.867 Ligand excluded by PLIP NAG.3: 2 residues within 4Å: Chain A: Q.22, N.55 Ligand excluded by PLIP NAG.4: 3 residues within 4Å: Chain A: N.1070, T.1072, F.1075 Ligand excluded by PLIP NAG.5: 3 residues within 4Å: Chain A: N.99, E.121, F.147 Ligand excluded by PLIP NAG.6: 4 residues within 4Å: Chain A: N.109, T.111, N.112, V.114 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain A: N.148 Chain B: A.329 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain A: S.95, T.96, N.217 Ligand excluded by PLIP NAG.9: 4 residues within 4Å: Chain A: D.257, E.258, N.259 Chain B: R.534 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: N.308, K.556 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: N.320, S.348 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: N.347 Chain B: Y.432, Y.465 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: N.592 Chain C: M.806 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: N.681, G.1103 Ligand excluded by PLIP NAG.15: 5 residues within 4Å: Chain A: N.689, F.690, Q.894, Q.898, Q.1043 Ligand excluded by PLIP NAG.16: 4 residues within 4Å: Chain A: Y.768, N.773, S.775, Q.776 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain A: N.1106 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: Q.867 Chain B: A.678, N.1046 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain B: Q.22, N.55 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain B: N.1070, T.1072, F.1075 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: N.99, E.121, F.147 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain B: N.109, S.110, N.112, I.154 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain B: F.147, N.148 Chain C: A.329 Ligand excluded by PLIP NAG.26: 5 residues within 4Å: Chain B: T.96, N.217 Chain C: K.437, R.439, E.442 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: E.258, N.259 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: N.308, K.556 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.320 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: N.347 Chain C: Y.432, Y.465 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain A: M.806, Q.808 Chain B: N.592, T.594 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain B: N.689, Q.898, Q.1043 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain B: Y.768, N.773, S.775, Q.776 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain B: N.1106 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain C: N.1046 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: Q.22, N.55 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain C: N.1070, T.1072, F.1075 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain C: N.99, E.121, F.147 Ligands: NAG.42 Ligand excluded by PLIP NAG.41: 6 residues within 4Å: Chain C: N.109, S.110, T.111, N.112, V.114, I.154 Ligand excluded by PLIP NAG.42: 5 residues within 4Å: Chain A: A.329, I.445 Chain C: F.147, N.148 Ligands: NAG.40 Ligand excluded by PLIP NAG.43: 5 residues within 4Å: Chain A: R.439 Chain C: S.95, T.96, N.217, T.219 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain A: R.534 Chain C: D.257, E.258, N.259 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain C: N.308, K.556 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain A: Y.432, Y.465 Chain C: N.347 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain B: M.806 Chain C: N.592 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain C: N.681 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain C: N.689, Q.894, Q.1043 Ligand excluded by PLIP NAG.50: 4 residues within 4Å: Chain C: Y.768, N.773, S.775, Q.776 Ligand excluded by PLIP NAG.51: 1 residues within 4Å: Chain C: N.1106 Ligand excluded by PLIP

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

BLA.18: 12 residues within 4Å: Chain A: N.86, V.88, R.89, W.91, N.108, V.113, F.158, R.173, F.175, K.188, I.209, F.210 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:N.86, A:W.91, A:K.188, A:I.209, A:F.210 Hydrogen bonds: A:N.108, A:K.188 pi-Cation interactions: A:R.173 BLA.35: 10 residues within 4Å: Chain B: V.88, R.89, W.91, N.108, V.113, F.158, R.173, F.175, K.188, I.209 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:R.89, B:W.91, B:F.175, B:K.188, B:I.209 pi-Cation interactions: B:K.188 BLA.52: 10 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 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:N.86, C:W.91, C:K.188, C:I.209 Hydrogen bonds: C:N.108 pi-Cation interactions: 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
B

B
A

C
C

Spike glycoprotein

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