SMTL ID : 6u7k.1

Prefusion structure of PEDV spike

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

3 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN.1: 14 residues within 4Å: Chain A: L.259, N.261, R.311, E.314, K.399, Y.400, D.402, Y.404, H.412, L.415, N.442 Chain C: R.815, Q.818, I.1073 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.815 NAG-NAG-BMA-MAN-MAN-MAN.6: 12 residues within 4Å: Chain A: R.815 Chain B: L.259, N.261, N.273, E.314, K.399, Y.400, D.402, Y.404, H.412, L.415, N.442 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.815, A:R.815 NAG-NAG-BMA-MAN-MAN-MAN.11: 10 residues within 4Å: Chain B: R.815 Chain C: L.259, N.261, E.314, Y.400, D.402, Y.404, L.415, N.442, F.443 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.273

12 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 4 residues within 4Å: Chain A: A.43, N.321, R.393, D.431 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: F.509, N.511, N.534, F.551 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 7 residues within 4Å: Chain A: T.636, D.637, S.639, M.641, N.685, T.687, S.688 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain A: N.870, N.873 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain B: A.43, K.286, N.321, R.393, D.431 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.43 Hydrogen bonds: B:A.43 NAG-NAG.8: 4 residues within 4Å: Chain B: F.509, N.511, T.549, F.551 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 7 residues within 4Å: Chain B: T.636, D.637, S.639, M.641, N.685, T.687, S.688 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain B: N.870, N.873 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain C: N.321, R.393, D.431 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain C: F.509, N.511, N.534, F.551 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 7 residues within 4Å: Chain C: T.636, D.637, S.639, M.641, N.685, T.687, S.688 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 2 residues within 4Å: Chain C: N.870, N.873 No protein-ligand interaction detected (PLIP)

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

NAG.16: 2 residues within 4Å: Chain A: N.213, Y.223 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain A: N.297 Ligand excluded by PLIP NAG.18: 6 residues within 4Å: Chain A: H.335, G.339, N.341, D.375, T.376, Y.377 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain A: N.348 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: Y.181, N.422 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain A: N.553 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain A: N.664 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: N.723, N.736 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain A: N.740 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: N.778, L.1191, Q.1192 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain A: T.783, N.784, D.1159, V.1161 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain A: S.1002, N.1006 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain A: Y.1194, N.1229 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: N.213, Y.223 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain B: N.297 Ligand excluded by PLIP NAG.31: 6 residues within 4Å: Chain B: H.335, G.339, N.341, D.375, T.376, Y.377 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: N.348, A.363 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain B: Y.181, A.328, E.329, N.422 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain B: N.553 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain B: N.664 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain B: N.723, N.736 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain B: N.740 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain B: N.778, L.1191, Q.1192 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain B: N.784, D.1159, V.1161 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain B: S.1002, N.1006 Ligand excluded by PLIP NAG.41: 6 residues within 4Å: Chain B: C.1170, C.1223, V.1224, V.1225, Y.1227, N.1229 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain C: N.213 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain C: F.296, N.297, K.399 Ligand excluded by PLIP NAG.44: 5 residues within 4Å: Chain C: H.335, G.339, N.341, D.375, T.376 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain C: N.348, A.363, V.366 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain C: Y.181, E.329, N.422 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain C: N.553 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain C: N.664 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain C: N.723, N.736 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain C: N.740 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain C: N.778, L.1191, Q.1192 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain C: T.783, N.784, D.1159 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain C: S.1002, G.1005, N.1006 Ligand excluded by PLIP NAG.54: 3 residues within 4Å: Chain C: Y.1194, V.1225, N.1229 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wrapp, D. et al., The 3.1-Angstrom Cryo-electron Microscopy Structure of the Porcine Epidemic Diarrhea Virus Spike Protein in the Prefusion Conformation. J.Virol. (2019)

Release Date

2019-09-18

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein