SMTL ID : 8xyh.1

Cryo-EM structure of BANAL-20-52 spike protein (6P)

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: 5 residues within 4Å: Chain A: N.122, T.124, N.125, V.127, V.171 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.171 NAG-NAG.2: 7 residues within 4Å: Chain B: N.122, A.123, T.124, N.125, V.127, E.154, V.171 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 7 residues within 4Å: Chain C: N.122, A.123, T.124, N.125, V.127, V.171, S.172 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:V.171 Hydrogen bonds: C:N.125

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

NAG.4: 2 residues within 4Å: Chain A: N.30, F.59 Ligand excluded by PLIP NAG.5: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.6: 4 residues within 4Å: Chain A: H.146, N.148, N.149, S.151 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain A: N.165 Chain C: Y.351 Ligand excluded by PLIP NAG.8: 7 residues within 4Å: Chain A: N.234, T.236 Chain C: R.457, S.459, N.460, L.461, K.462 Ligand excluded by PLIP NAG.9: 2 residues within 4Å: Chain A: N.331, Q.580 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: N.343, S.371 Ligand excluded by PLIP NAG.11: 4 residues within 4Å: Chain A: V.367, N.370 Chain C: L.455, F.456 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: N.616, Q.644 Chain B: I.830 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: N.705, P.1075 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain A: N.713, F.714, Q.922, Q.1067 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: N.797, S.799, Q.800 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: N.1094, F.1099 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: V.16, N.17, N.137 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: N.280, E.281, N.282 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain B: N.30 Ligand excluded by PLIP NAG.21: 5 residues within 4Å: Chain B: Y.28, T.29, N.30, S.60, N.61 Ligand excluded by PLIP NAG.22: 5 residues within 4Å: Chain B: H.146, N.148, N.149, S.151, M.153 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: Y.351 Chain B: N.164, N.165 Ligand excluded by PLIP NAG.24: 7 residues within 4Å: Chain A: R.457, S.459, N.460, K.462, E.465 Chain B: T.108, N.234 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain B: N.280, E.281, N.282 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain B: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: N.343, S.371, T.372 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain A: F.456, Y.489, Q.493 Chain B: N.370 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: N.616, Q.644 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: N.705, P.1075 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: N.713, Q.1067 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: G.795, N.797 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain B: N.1094, H.1097, F.1099 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain B: N.17, N.137 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: N.30, F.59 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain C: Y.28, T.29, N.30, N.61 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain B: Y.351, I.468 Chain C: N.164, N.165 Ligand excluded by PLIP NAG.39: 6 residues within 4Å: Chain B: R.457, N.460, K.462, E.465 Chain C: T.108, N.234 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain C: N.280, N.282, T.284 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: N.343, S.371 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain B: F.456, Y.489 Chain C: N.370 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain A: I.830 Chain C: N.616, Q.644, T.645 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain A: K.791 Chain C: N.705, N.706, T.1073 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain C: N.713, N.915 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain C: N.797, S.799, Q.800 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain C: N.1094, H.1097, F.1099 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain C: V.16, N.17 Ligand excluded by PLIP NAG.49: 4 residues within 4Å: Chain C: P.330, N.331, P.579, Q.580 Ligand excluded by PLIP NAG.51: 5 residues within 4Å: Chain C: H.146, N.148, N.149, S.151, M.153 Ligand excluded by PLIP

3 x EIC: LINOLEIC ACID(Non-covalent)

EIC.18: 14 residues within 4Å: Chain A: P.337, F.338, F.342, I.358, A.363, Y.365, F.374, F.377, L.387, F.392, V.395, L.513, F.515, V.524 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:F.338, A:F.338, A:F.342, A:I.358, A:A.363, A:Y.365, A:Y.365, A:L.387, A:L.387, A:F.392, A:V.395, A:L.513, A:L.513, A:F.515, A:V.524 EIC.35: 13 residues within 4Å: Chain B: C.336, F.338, F.342, I.358, Y.365, F.374, F.377, F.392, V.395, I.434, L.513, F.515, V.524 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:F.338, B:F.342, B:I.358, B:I.358, B:Y.365, B:F.377, B:F.392, B:F.392, B:V.395, B:V.395, B:F.515, B:V.524 EIC.50: 9 residues within 4Å: Chain C: F.342, I.358, Y.365, F.377, L.387, F.392, L.513, F.515, V.524 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:F.342, C:Y.365, C:F.377, C:L.387, C:F.392, C:F.392, C:F.392, C:L.513, C:F.515, C:V.524

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, Z.P. et al., Structural resemblances of bat-origin coronaviruses CX1 and BANAL-20-52 spikes provide further evidence on bat origination of SARS-CoV-2. To Be Published

Release Date

2025-01-22

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein