SMTL ID : 9k6z.1

SARS-CoV-2 related bat coronavirus BANAL-52 spike in the locked state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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

NAG.1: 5 residues within 4Å: Chain A: N.122, N.125, V.127, E.154, V.171 Ligand excluded by PLIP NAG.2: 2 residues within 4Å: Chain A: E.281, N.282 Ligand excluded by PLIP NAG.3: 2 residues within 4Å: Chain A: N.331, Q.580 Ligand excluded by PLIP NAG.4: 3 residues within 4Å: Chain A: N.370 Chain C: F.456, Y.489 Ligand excluded by PLIP NAG.5: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.6: 1 residues within 4Å: Chain A: N.713 Ligand excluded by PLIP NAG.7: 4 residues within 4Å: Chain A: N.1094, G.1095, H.1097, F.1099 Ligand excluded by PLIP NAG.8: 1 residues within 4Å: Chain A: N.1130 Ligand excluded by PLIP NAG.9: 5 residues within 4Å: Chain A: N.234, T.236 Chain C: R.457, N.460, K.462 Ligand excluded by PLIP NAG.10: 1 residues within 4Å: Chain A: N.343 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: N.616, T.618, E.619 Ligand excluded by PLIP NAG.12: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: N.705, G.1127 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain A: C.15, V.16, N.17, N.137 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: N.165 Chain C: A.352, I.468 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain A: N.30 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain A: H.146, N.149, S.151, M.153 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain B: N.122, N.125, V.127, E.154 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain B: E.281, N.282 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: N.331, Q.580 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: F.456, Y.489 Chain B: N.370 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain B: N.713 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain B: N.1094, G.1095, H.1097, F.1099 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain B: N.1130 Ligand excluded by PLIP NAG.28: 5 residues within 4Å: Chain A: R.457, N.460, K.462 Chain B: N.234, T.236 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.343 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: N.616, T.618, E.619 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: N.705, G.1127 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain B: C.15, V.16, N.17, N.137 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain A: A.352, I.468 Chain B: N.165 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain B: N.30 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain B: H.146, N.149, S.151 Ligand excluded by PLIP NAG.39: 5 residues within 4Å: Chain C: N.122, N.125, V.127, E.154, V.171 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: E.281, N.282 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: N.331, Q.580 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: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain C: N.713 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain C: N.1094, G.1095, H.1097, F.1099 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain C: N.1130 Ligand excluded by PLIP NAG.47: 5 residues within 4Å: Chain B: R.457, N.460, K.462 Chain C: N.234, T.236 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain C: N.343 Ligand excluded by PLIP NAG.49: 4 residues within 4Å: Chain A: Q.832 Chain C: N.616, T.618, E.619 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain C: N.705, G.1127 Ligand excluded by PLIP NAG.52: 4 residues within 4Å: Chain C: C.15, V.16, N.17, N.137 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.54: 3 residues within 4Å: Chain B: A.352, I.468 Chain C: N.165 Ligand excluded by PLIP NAG.55: 1 residues within 4Å: Chain C: N.30 Ligand excluded by PLIP NAG.56: 4 residues within 4Å: Chain C: H.146, N.149, S.151, M.153 Ligand excluded by PLIP

3 x EIC: LINOLEIC ACID(Non-covalent)

EIC.19: 14 residues within 4Å: Chain A: C.336, F.338, V.341, A.363, Y.365, Y.369, F.374, F.377, F.392, V.395, I.434, L.513 Chain C: R.408, Q.409 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:F.338, A:V.341, A:A.363, A:Y.365, A:Y.365, A:F.374, A:F.374, A:F.392, A:V.395, A:V.395, A:I.434, A:L.513 Hydrogen bonds: C:R.408, C:Q.409 EIC.38: 11 residues within 4Å: Chain A: R.408, Q.409 Chain B: F.338, V.341, A.363, Y.365, Y.369, F.374, F.377, F.392, I.434 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.338, B:F.338, B:V.341, B:A.363, B:Y.365, B:Y.365, B:F.374, B:F.374, B:F.392, B:I.434 Hydrogen bonds: A:R.408, A:Q.409 EIC.57: 13 residues within 4Å: Chain B: R.408, Q.409 Chain C: F.338, V.341, I.358, A.363, Y.365, Y.369, F.374, F.377, F.392, I.434, L.513 11 PLIP interactions: 2 interactions with chain B, 9 interactions with chain C Hydrogen bonds: B:R.408, B:Q.409 Hydrophobic interactions: C:F.338, C:F.338, C:V.341, C:I.358, C:F.374, C:F.374, C:F.392, C:I.434, C:L.513

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, Q.Q. et al., Characteristics of Spike Activation,Structure and Host Proteases Adaption Revealed Limitations for SARS-CoV-2 related Coronavirus Cell Entry. To Be Published

Release Date

2025-07-23

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein