SMTL ID : 7u6r.1

Cryo-EM structure of PDF-2180 Spike glycoprotein

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: 6 residues within 4Å: Chain A: N.414, T.416, L.417, S.420, K.585, Q.586 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.170 Chain B: Q.525, V.528, T.529 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain B: N.414, T.416, L.417, S.420, K.585, Q.586 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain B: N.170 Chain C: Q.525, V.528, T.529 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 6 residues within 4Å: Chain C: N.414, T.416, L.417, S.420, K.585, Q.586 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: Q.525, V.528, T.529 Chain C: N.170 No protein-ligand interaction detected (PLIP)

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

NAG.7: 2 residues within 4Å: Chain A: N.70, V.333 Ligand excluded by PLIP NAG.8: 4 residues within 4Å: Chain A: P.40, N.108, Y.111, Y.112 Ligand excluded by PLIP NAG.9: 2 residues within 4Å: Chain A: G.157, N.158 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: N.862, L.865 Ligand excluded by PLIP NAG.11: 4 residues within 4Å: Chain A: N.388, T.390, D.391, E.395 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: N.594, T.596 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: N.1167, R.1171 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: L.190, Q.192, N.240 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: E.246, N.248 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: N.777, K.992 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain A: V.1201, F.1203, Q.1204, N.1205 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: E.717, T.718, N.719 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: N.489, S.491 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain B: N.70, V.333 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain B: P.40, N.108, Y.111, Y.112 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: G.157, N.158 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: N.862, L.865 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain B: N.388, T.390, D.391, E.395 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: N.594, T.596 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: N.1167, R.1171 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: L.190, Q.192, N.240 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: E.246, N.248 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: N.777, K.992 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain B: V.1201, F.1203, Q.1204, N.1205 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain B: E.717, T.718, N.719 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: N.489, S.491 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: N.70, V.333 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain C: P.40, N.108, Y.111, Y.112 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: G.157, N.158 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: N.862, L.865 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain C: N.388, T.390, D.391, E.395 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: N.594, T.596 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: N.1167, R.1171 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain C: L.190, Q.192, N.240 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: E.246, N.248 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain C: N.777, K.992 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain C: V.1201, F.1203, Q.1204, N.1205 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain C: E.717, T.718, N.719 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain C: N.489, S.491 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xiong, Q. et al., Close relatives of MERS-CoV in bats use ACE2 as their functional receptors. Nature (2022)

Release Date

2022-11-30

Peptides

PDF-2180 Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

PDF-2180 Spike glycoprotein