SMTL ID : 8zy1.1

Sarbecovirus BM48-31 Spike Trimer in a Locked Conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

6 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: 3 residues within 4Å: Chain A: D.782, N.787, S.789 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: N.361 Chain B: Y.476 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain B: D.782, N.787, S.789 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain B: N.361 Chain C: Y.476 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain C: D.782, N.787, S.789 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain A: Y.476 Chain C: N.361 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.2: 8 residues within 4Å: Chain A: S.112, N.231 Chain B: R.445, H.446, K.448, P.463, S.464, G.465 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.446, B:P.463 NAG-NAG-BMA-MAN.5: 7 residues within 4Å: Chain B: S.112, N.231, Y.234 Chain C: R.445, H.446, K.448, P.463 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.446 NAG-NAG-BMA-MAN.8: 8 residues within 4Å: Chain A: R.445, H.446, K.448, P.463, G.465 Chain C: S.112, N.231, Q.516 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:Q.516, A:H.446

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

NAG.10: 2 residues within 4Å: Chain A: N.322, K.567 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: N.603, T.605 Chain C: Q.822 Ligand excluded by PLIP NAG.12: 1 residues within 4Å: Chain A: N.646 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain A: N.695 Ligand excluded by PLIP NAG.14: 1 residues within 4Å: Chain A: N.703 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: N.1060 Chain C: Q.881 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: Q.33, N.66, H.618 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain A: N.116 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: D.271, E.272, N.273 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: N.334, S.363, A.364 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: N.1084, H.1087, F.1089 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain A: N.1120 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain A: N.163 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: N.322, K.567 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: N.603, T.605 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain B: N.646 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain B: N.695 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: N.703, Q.1057 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.1060 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: Q.33, N.66, H.618 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain B: N.116, N.138, S.160 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain B: D.271, E.272, N.273 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain B: N.334, S.362, S.363 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain B: N.1084, T.1086, H.1087 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain B: N.1120 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain B: N.163 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: N.322, K.567 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: N.603, T.605 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain C: N.646 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain C: N.695 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: N.703, Q.1057 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain C: N.1060 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain C: N.66, H.618 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain C: N.116, N.138 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain C: D.271, E.272, N.273 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain C: N.334, S.362, S.363 Ligand excluded by PLIP NAG.49: 4 residues within 4Å: Chain C: N.1084, T.1086, H.1087, F.1089 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain C: N.1120 Ligand excluded by PLIP NAG.51: 1 residues within 4Å: Chain C: N.163 Ligand excluded by PLIP

3 x EIC: LINOLEIC ACID(Non-covalent)

EIC.23: 10 residues within 4Å: Chain A: F.329, A.354, Y.356, L.359, F.366, F.369, V.387, I.426, L.500 Chain B: R.400 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.329, A:A.354, A:L.359, A:F.366, A:F.369, A:F.369, A:V.387, A:I.426, A:L.500 Salt bridges: B:R.400 EIC.37: 12 residues within 4Å: Chain B: C.327, F.329, V.332, I.349, A.354, Y.356, L.359, F.366, F.369, F.384, L.500 Chain C: R.400 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:F.329, B:F.329, B:V.332, B:I.349, B:A.354, B:Y.356, B:F.366, B:F.366, B:F.369, B:F.384, B:L.500 Salt bridges: C:R.400 EIC.38: 18 residues within 4Å: Chain A: R.400, T.407, G.408 Chain C: C.327, F.329, F.333, I.349, A.354, Y.356, L.359, F.366, F.369, L.379, F.384, V.387, I.426, L.500, F.502 19 PLIP interactions: 18 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:F.329, C:F.329, C:F.329, C:F.333, C:I.349, C:A.354, C:Y.356, C:Y.356, C:L.359, C:F.366, C:F.369, C:F.369, C:L.379, C:F.384, C:V.387, C:I.426, C:F.502, C:F.502 Salt bridges: A:R.400

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, J. et al., SARS-related coronavirus S-protein structures reveal synergistic RBM interactions underpinning high-affinity human ACE2 binding. Sci Adv (2025)

Release Date

2025-02-05

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein