SMTL ID : 8h10.1

Structure of SARS-CoV-1 Spike Protein with Engineered x1 Disulfide (S370C and D967C), Locked-2 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, T.219 Chain C: R.434, H.435, R.439, E.442 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 7 residues within 4Å: Chain A: R.434, H.435, R.439, E.442 Chain B: S.95, N.217, T.219 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 7 residues within 4Å: Chain B: R.434, H.435, K.437, R.439 Chain C: S.95, N.217, T.219 No protein-ligand interaction detected (PLIP)

42 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: 3 residues within 4Å: Chain A: N.99, E.121, F.147 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain A: N.109, T.111 Ligand excluded by PLIP NAG.8: 1 residues within 4Å: Chain A: N.148 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain A: E.258, N.259 Chain C: 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 C: Y.432, Y.465 Ligand excluded by PLIP NAG.12: 1 residues within 4Å: Chain A: N.592 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: N.681, G.1103 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: N.689, Q.894, Q.1043 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 B: Q.867 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.1106 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain B: Q.22, N.55 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain B: N.1070, T.1072, F.1075 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain B: N.99, E.121, F.147 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: N.109, T.111 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain B: N.148 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: R.534 Chain B: E.258, N.259 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: N.308, K.556 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: 1 residues within 4Å: Chain B: N.592 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: N.681, G.1103 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: N.689, Q.894, Q.1043 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain B: Y.768, N.773, S.775, Q.776 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: N.1046 Chain C: Q.867 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain B: N.1106 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: Q.22, N.55 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: N.1070, T.1072, F.1075 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain C: N.99, E.121, F.147 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: N.109, T.111 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain B: Y.328 Chain C: N.148 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain B: R.534 Chain C: E.258, N.259 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: N.308, K.556 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain B: Y.432, Y.465 Chain C: N.347 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain C: N.592 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain C: N.681, G.1103 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain C: N.689, Q.894, Q.1043 Ligand excluded by PLIP NAG.48: 4 residues within 4Å: Chain C: Y.768, N.773, S.775, Q.776 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain A: Q.867 Chain C: N.1046 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.17: 15 residues within 4Å: Chain A: E.83, N.86, V.88, R.89, G.90, W.91, I.106, I.107, N.108, V.113, R.173, F.175, K.188, I.209, F.210 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:N.86, A:V.88, A:W.91, A:I.106, A:N.108, A:V.113, A:K.188, A:I.209, A:F.210 Hydrogen bonds: A:N.108, A:R.173 pi-Cation interactions: A:R.173 BLA.33: 15 residues within 4Å: Chain B: E.83, N.86, V.88, R.89, G.90, W.91, I.106, I.107, N.108, V.113, R.173, F.175, K.188, I.209, F.210 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:N.86, B:V.88, B:W.91, B:I.106, B:N.108, B:V.113, B:K.188, B:I.209, B:F.210 Hydrogen bonds: B:N.108, B:R.173 pi-Cation interactions: B:R.173 BLA.50: 15 residues within 4Å: Chain C: E.83, N.86, V.88, R.89, G.90, W.91, I.106, I.107, N.108, V.113, R.173, F.175, K.188, I.209, F.210 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:N.86, C:V.88, C:W.91, C:I.106, C:N.108, C:V.113, C:K.188, C:I.209, C:F.210 Hydrogen bonds: C:N.108, C:R.173 pi-Cation interactions: C:R.173

3 x EIC: LINOLEIC ACID(Non-covalent)

EIC.19: 13 residues within 4Å: Chain A: R.385, T.392, G.393, V.394 Chain B: C.313, I.335, A.340, Y.342, Y.346, F.351, F.354, F.369, L.489 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.335, B:Y.342, B:Y.342, B:Y.346, B:F.369, B:L.489 Hydrogen bonds: A:V.394 Salt bridges: A:R.385 EIC.35: 13 residues within 4Å: Chain B: R.385, T.392, G.393, V.394 Chain C: C.313, I.335, A.340, Y.342, Y.346, F.351, F.354, F.369, L.489 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:I.335, C:Y.342, C:Y.342, C:Y.346, C:F.369, C:L.489 Hydrogen bonds: B:V.394 Salt bridges: B:R.385 EIC.36: 13 residues within 4Å: Chain A: C.313, I.335, A.340, Y.342, Y.346, F.351, F.354, F.369, L.489 Chain C: R.385, T.392, G.393, V.394 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:I.335, A:Y.342, A:Y.342, A:Y.346, A:F.369, A:L.489 Hydrogen bonds: C:Q.386, C:V.394 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

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