SMTL ID : 8h0z.1

Structure of SARS-CoV-1 Spike Protein with Engineered x1 Disulfide (S370C and D967C), Locked-122 Conformation

Coordinates

PDB Format Compare

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.95, N.217 Chain B: R.434, H.435, K.437, R.439, E.442 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 6 residues within 4Å: Chain B: S.95, N.217 Chain C: R.434, H.435, K.437, R.439 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain A: R.434, H.435, R.439, E.442 Chain C: S.95, N.217 No protein-ligand interaction detected (PLIP)

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

NAG.4: 2 residues within 4Å: Chain A: Q.22, N.55 Ligand excluded by PLIP NAG.5: 3 residues within 4Å: Chain A: N.1070, T.1072, F.1075 Ligand excluded by PLIP NAG.6: 2 residues within 4Å: Chain A: N.99, E.121 Ligand excluded by PLIP NAG.7: 5 residues within 4Å: Chain A: N.109, S.110, T.111, N.112, I.154 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain A: F.147, N.148 Chain B: A.329 Ligand excluded by PLIP NAG.9: 2 residues within 4Å: Chain A: 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: 3 residues within 4Å: Chain A: N.347 Chain B: Y.432, L.433 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: N.592, Q.620 Chain C: Q.808 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain A: N.681 Ligand excluded by PLIP NAG.14: 1 residues within 4Å: Chain A: N.689 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain A: Y.768, N.773, S.775, Q.776 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: N.1046 Chain C: Q.867 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain B: N.55 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain B: R.1045, N.1070, T.1072, F.1075 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: N.99, E.121 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain B: N.109, S.110, T.111, V.114 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain B: N.148 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: E.258, N.259 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: N.308, K.556 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: N.347 Chain C: Y.432, Y.465 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain A: M.806 Chain B: N.592, T.594 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: N.681, G.1103 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: N.689, Q.894 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain B: Y.768, N.773, Q.776 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: E.1044, N.1046 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain C: Q.22, H.23, N.55 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain C: N.1070, T.1072, F.1075 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: N.99, E.121 Ligand excluded by PLIP NAG.38: 5 residues within 4Å: Chain C: N.109, S.110, T.111, N.112, I.154 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain A: A.329 Chain C: N.148 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: N.308, K.556 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain A: Y.432, Y.465 Chain C: N.347 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain B: Q.808 Chain C: N.592, Q.620 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain C: N.681 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: N.689, Q.894 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain C: Y.768, N.773, S.775, Q.776 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain C: E.1044, N.1046 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.17: 10 residues within 4Å: Chain A: N.86, V.88, R.89, G.90, W.91, N.108, F.158, R.173, F.175, K.188 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.91, A:F.158 Hydrogen bonds: A:K.188 pi-Cation interactions: A:R.173 BLA.34: 8 residues within 4Å: Chain B: V.88, R.89, G.90, W.91, N.108, R.173, K.188, Y.190 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.91 Hydrogen bonds: B:N.108 pi-Cation interactions: B:R.173 BLA.48: 12 residues within 4Å: Chain C: N.86, V.88, R.89, G.90, 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:F.175, C:I.209, C:I.209, C:F.210 Hydrogen bonds: C:N.86, C:N.108 Salt bridges: C:K.207 pi-Cation interactions: C:R.173, C:K.188

3 x EIC: LINOLEIC ACID(Non-covalent)

EIC.18: 14 residues within 4Å: Chain A: R.385, T.392, G.393 Chain C: C.313, P.314, V.318, I.335, A.340, Y.342, F.351, F.354, F.369, L.489, F.491 15 PLIP interactions: 14 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:P.314, C:V.318, C:I.335, C:A.340, C:Y.342, C:Y.342, C:F.351, C:F.354, C:F.369, C:F.369, C:L.489, C:L.489, C:F.491, C:F.491 Salt bridges: A:R.385 EIC.19: 14 residues within 4Å: Chain A: C.313, F.315, I.335, A.340, Y.342, F.351, F.354, L.364, F.369, V.372, L.489 Chain B: R.385, T.392, G.393 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.315, A:I.335, A:A.340, A:Y.342, A:Y.342, A:Y.342, A:F.351, A:F.351, A:L.364, A:F.369, A:V.372, A:L.489 Hydrogen bonds: B:Q.386 Salt bridges: B:R.385 EIC.20: 11 residues within 4Å: Chain B: C.313, P.314, V.318, I.335, A.340, Y.342, Y.346, F.351, F.354, F.369, V.372 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:V.318, B:I.335, B:A.340, B:Y.342, B:Y.342, B:F.351, B:F.354, B:F.354, B:F.369, B:V.372

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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