SMTL ID : 8zy2.1

Sarbecovirus BANAL-20-52 Spike Trimer in a Locked Conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

21 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: 6 residues within 4Å: Chain A: N.122, T.124, N.125, V.127, F.157, P.174 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 8 residues within 4Å: Chain A: T.108, N.234, T.236 Chain B: R.457, K.458, S.459, N.460, E.465 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.713, L.918, Q.1067 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.918 NAG-NAG.4: 3 residues within 4Å: Chain A: N.797, S.799, Q.800 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: N.1094, T.1096, H.1097, F.1099 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 1 residues within 4Å: Chain A: N.1130 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain A: H.146, N.148, N.149, S.151, M.153 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 6 residues within 4Å: Chain B: N.122, T.124, N.125, V.127, F.157, P.174 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 8 residues within 4Å: Chain B: T.108, N.234, T.236 Chain C: R.457, K.458, S.459, N.460, E.465 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain B: N.713, L.918, Q.1067 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.918 NAG-NAG.11: 3 residues within 4Å: Chain B: N.797, S.799, Q.800 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain B: N.1094, T.1096, H.1097, F.1099 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 1 residues within 4Å: Chain B: N.1130 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 5 residues within 4Å: Chain B: H.146, N.148, N.149, S.151, M.153 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 6 residues within 4Å: Chain C: N.122, T.124, N.125, V.127, F.157, P.174 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 8 residues within 4Å: Chain A: R.457, K.458, S.459, N.460, E.465 Chain C: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain C: N.713, L.918, Q.1067 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.918 NAG-NAG.18: 3 residues within 4Å: Chain C: N.797, S.799, Q.800 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 4 residues within 4Å: Chain C: N.1094, T.1096, H.1097, F.1099 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 1 residues within 4Å: Chain C: N.1130 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 5 residues within 4Å: Chain C: H.146, N.148, N.149, S.151, M.153 No protein-ligand interaction detected (PLIP)

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

NAG.22: 2 residues within 4Å: Chain A: N.331, Q.580 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: N.616, E.619, Q.644 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain A: N.705, G.1127 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: A.702, E.1068, N.1070 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain A: N.165 Chain B: Y.351 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain A: N.280, E.281, N.282 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain A: N.343 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain A: C.15, N.17, N.137 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain A: N.370 Chain B: Q.493 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain A: N.30 Ligands: NAG.32 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain A: Y.28, N.61 Ligands: NAG.31 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain B: N.331, Q.580 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain B: N.616, E.619 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain B: N.705, G.1127 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain B: A.702, E.1068, N.1070 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain B: N.165 Chain C: Y.351 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain B: N.280, E.281, N.282 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain B: N.343 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain B: C.15, N.17, N.137 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain B: N.370 Chain C: Q.493 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain B: N.30 Ligands: NAG.46 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain B: Y.28, N.61 Ligands: NAG.45 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain C: N.331, Q.580, T.581 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain C: N.616, E.619 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain C: N.705, G.1127 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain C: A.702, E.1068, N.1070 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain A: Y.351 Chain C: N.165 Ligand excluded by PLIP NAG.54: 4 residues within 4Å: Chain A: K.558 Chain C: N.280, E.281, N.282 Ligand excluded by PLIP NAG.55: 2 residues within 4Å: Chain C: N.343, S.371 Ligand excluded by PLIP NAG.56: 3 residues within 4Å: Chain C: C.15, N.17, N.137 Ligand excluded by PLIP NAG.57: 2 residues within 4Å: Chain A: Q.493 Chain C: N.370 Ligand excluded by PLIP NAG.58: 2 residues within 4Å: Chain C: N.30 Ligands: NAG.59 Ligand excluded by PLIP NAG.59: 3 residues within 4Å: Chain C: Y.28, N.61 Ligands: NAG.58 Ligand excluded by PLIP

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

BLA.33: 6 residues within 4Å: Chain A: E.96, I.101, N.121, R.190, F.192, L.226 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.226 Hydrogen bonds: A:N.121 BLA.47: 8 residues within 4Å: Chain B: E.96, N.99, I.101, N.121, V.126, R.190, F.192, L.226 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:N.99, B:V.126, B:L.226 Hydrogen bonds: B:N.121 BLA.60: 7 residues within 4Å: Chain C: E.96, I.101, N.121, V.126, R.190, F.192, L.226 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:V.126, C:L.226 Hydrogen bonds: C:N.121

3 x EIC: LINOLEIC ACID(Non-covalent)

EIC.34: 16 residues within 4Å: Chain A: R.408, Q.409, T.415, G.416 Chain C: F.338, V.341, I.358, A.363, Y.365, L.368, F.374, F.377, F.392, V.395, I.434, F.515 17 PLIP interactions: 15 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:F.338, C:F.338, C:V.341, C:I.358, C:Y.365, C:Y.365, C:Y.365, C:L.368, C:F.374, C:F.374, C:F.377, C:F.392, C:V.395, C:I.434, C:F.515 Hydrogen bonds: A:T.415 Salt bridges: A:R.408 EIC.35: 19 residues within 4Å: Chain A: C.336, P.337, F.338, V.341, I.358, A.363, Y.365, Y.369, F.374, F.377, F.392, I.434, L.513, F.515, V.524 Chain B: R.408, Q.409, T.415, G.416 17 PLIP interactions: 2 interactions with chain B, 15 interactions with chain A Hydrogen bonds: B:T.415 Salt bridges: B:R.408 Hydrophobic interactions: A:F.338, A:F.338, A:V.341, A:I.358, A:A.363, A:Y.365, A:Y.365, A:Y.365, A:Y.369, A:F.374, A:F.377, A:F.377, A:I.434, A:F.515, A:V.524 EIC.48: 18 residues within 4Å: Chain B: P.337, F.338, V.341, I.358, A.363, Y.365, L.368, F.374, F.377, F.392, I.434, L.513, F.515, V.524 Chain C: R.408, Q.409, T.415, G.416 22 PLIP interactions: 20 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:F.338, B:F.338, B:V.341, B:I.358, B:A.363, B:Y.365, B:Y.365, B:Y.365, B:L.368, B:F.374, B:F.374, B:F.377, B:F.377, B:F.392, B:I.434, B:L.513, B:L.513, B:F.515, B:F.515, B:V.524 Hydrogen bonds: C:T.415 Salt bridges: C:R.408

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