SMTL ID : 9jmp.1

Cryo-EM structure of GD-BatCoV (BtCoV/Ii/GD/2014-422) S-trimer

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.10 Å

Oligo State

homo-trimer

Ligands

9 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: 2 residues within 4Å: Chain A: N.69, V.333 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain A: D.20, S.21, W.185, N.226, L.229 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.20 NAG-NAG.4: 5 residues within 4Å: Chain A: N.414, T.416, K.417, M.591 Chain C: K.505 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain B: D.20, S.21, N.226, L.229 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.20, B:D.20 NAG-NAG.7: 4 residues within 4Å: Chain B: N.414, T.416, K.417, M.591 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain B: N.69 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 1 residues within 4Å: Chain C: N.69 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain B: K.505 Chain C: N.414, K.417, M.591 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 7 residues within 4Å: Chain C: D.20, S.21, G.22, W.185, N.226, L.229, I.244 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:I.244 Hydrogen bonds: C:D.20

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

NAG-NAG-BMA.2: 5 residues within 4Å: Chain A: N.130, E.253, N.254, A.255, Y.278 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 6 residues within 4Å: Chain B: G.126, N.130, E.253, N.254, A.255, Y.278 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.254 NAG-NAG-BMA.10: 6 residues within 4Å: Chain C: N.130, D.252, E.253, N.254, A.255, Y.278 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.278

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

NAG.13: 2 residues within 4Å: Chain A: N.159, G.163 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: N.52, S.54, K.55 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain A: N.248 Ligand excluded by PLIP NAG.16: 4 residues within 4Å: Chain A: L.712, Q.713, N.724, L.755 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: L.861, N.866, T.868 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: N.623, N.651 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain A: F.169, N.170 Chain C: N.532, P.535 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain B: N.52, S.54, K.55 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain A: Q.551 Chain B: N.159, G.163 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain B: Q.713, T.714, N.724, L.755 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain B: L.861, N.866, T.868 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: N.532, P.535 Chain B: N.170 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain B: N.623, C.624, T.625, N.651 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain B: N.248 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain C: L.712, Q.713, N.724, S.726 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain C: L.861, N.866, T.868 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain B: N.532, P.535 Chain C: N.170 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: R.183, N.248 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain C: N.623, N.651 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain B: S.550, Q.551 Chain C: N.159, G.163 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain C: N.52, S.54, K.55 Ligand excluded by PLIP

3 x EIC: LINOLEIC ACID(Non-covalent)

EIC.20: 19 residues within 4Å: Chain A: Y.459, S.464, A.465, G.466 Chain B: F.389, Y.413, L.415, L.418, L.419, F.422, V.424, F.427, P.434, L.445, V.447, I.484, A.486, F.575, I.577 17 PLIP interactions: 1 interactions with chain A, 16 interactions with chain B Hydrogen bonds: A:A.465 Hydrophobic interactions: B:F.389, B:L.415, B:L.415, B:L.418, B:F.422, B:V.424, B:V.424, B:L.445, B:V.447, B:I.484, B:I.484, B:A.486, B:F.575, B:F.575, B:I.577, B:I.577 EIC.28: 16 residues within 4Å: Chain B: Y.459, S.464, A.465, G.466 Chain C: L.415, L.418, L.419, F.422, V.424, F.427, P.434, I.437, V.447, I.484, F.575, I.577 14 PLIP interactions: 12 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:L.415, C:L.418, C:F.422, C:V.424, C:V.424, C:F.427, C:F.427, C:I.437, C:V.447, C:I.484, C:F.575, C:I.577 Hydrogen bonds: B:A.465, B:G.466 EIC.29: 17 residues within 4Å: Chain A: F.389, L.415, L.418, L.419, F.422, V.424, F.427, P.434, I.437, I.484, F.575, I.577 Chain C: S.458, Y.459, S.464, A.465, G.466 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:F.389, A:L.415, A:L.418, A:F.422, A:V.424, A:V.424, A:P.434, A:I.437, A:I.484, A:F.575, A:F.575, A:I.577 Hydrogen bonds: C:A.465

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yuan, H. et al., Structures and receptor binding activities of merbecovirus spike proteins reveal key signatures for human DPP4 adaptation. Sci Adv (2025)

Release Date

2025-06-18

Peptides

Spike glycoprotein,Fibritin: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein,Fibritin