SMTL ID : 6vv5.1

Cryo-EM structure of porcine epidemic diarrhea virus (PEDV) spike protein

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

3 x NAG- NAG- BMA- MAN- MAN- MAN- NAG- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-[alpha-D-mannopyranose-(1-6)]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-NAG-MAN.1: 14 residues within 4Å: Chain A: L.244, S.245, N.246, R.296, E.299, K.384, Y.385, D.387, Y.389, L.400 Chain B: R.800, Q.803, I.1058, L.1059 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.400 NAG-NAG-BMA-MAN-MAN-MAN-NAG-MAN.11: 14 residues within 4Å: Chain B: L.244, S.245, N.246, R.296, E.299, K.384, Y.385, D.387, Y.389, L.400 Chain C: R.800, Q.803, I.1058, L.1059 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.400 NAG-NAG-BMA-MAN-MAN-MAN-NAG-MAN.21: 14 residues within 4Å: Chain A: R.800, Q.803, I.1058, L.1059 Chain C: L.244, S.245, N.246, R.296, E.299, K.384, Y.385, D.387, Y.389, L.400 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.400

24 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: 6 residues within 4Å: Chain A: H.320, G.324, N.326, D.360, T.361, Y.362 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: F.494, N.496, N.519 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.494 NAG-NAG.4: 3 residues within 4Å: Chain A: S.500, F.536, N.538 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain A: N.708, S.709, N.721 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain A: R.711, G.723, S.724, N.725 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain A: T.768, N.769, D.1144, F.1145, V.1146 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain A: N.855, T.857, N.858 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain A: V.1209, V.1210, N.1214 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.1210 NAG-NAG.12: 6 residues within 4Å: Chain B: H.320, G.324, N.326, D.360, T.361, Y.362 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain B: F.494, N.496, N.519 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.494 NAG-NAG.14: 3 residues within 4Å: Chain B: S.500, F.536, N.538 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain B: N.708, S.709, N.721 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain B: R.711, G.723, S.724, N.725 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 5 residues within 4Å: Chain B: T.768, N.769, D.1144, F.1145, V.1146 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 3 residues within 4Å: Chain B: N.855, T.857, N.858 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 3 residues within 4Å: Chain B: V.1209, V.1210, N.1214 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.1210 NAG-NAG.22: 6 residues within 4Å: Chain C: H.320, G.324, N.326, D.360, T.361, Y.362 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 3 residues within 4Å: Chain C: F.494, N.496, N.519 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.494 NAG-NAG.24: 3 residues within 4Å: Chain C: S.500, F.536, N.538 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 3 residues within 4Å: Chain C: N.708, S.709, N.721 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 4 residues within 4Å: Chain C: R.711, G.723, S.724, N.725 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 5 residues within 4Å: Chain C: T.768, N.769, D.1144, F.1145, V.1146 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 3 residues within 4Å: Chain C: N.855, T.857, N.858 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 3 residues within 4Å: Chain C: V.1209, V.1210, N.1214 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.1210

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.5: 7 residues within 4Å: Chain A: D.622, S.624, F.625, M.626, N.670, T.672, S.673 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 7 residues within 4Å: Chain B: D.622, S.624, F.625, M.626, N.670, T.672, S.673 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.25: 7 residues within 4Å: Chain C: D.622, S.624, F.625, M.626, N.670, T.672, S.673 No protein-ligand interaction detected (PLIP)

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

NAG.31: 3 residues within 4Å: Chain A: V.28, N.198, T.200 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.28, A:N.198 NAG.32: 2 residues within 4Å: Chain A: N.282, Q.283 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.283 Hydrogen bonds: A:Q.283 NAG.33: 1 residues within 4Å: Chain A: N.649 No protein-ligand interaction detected (PLIP) NAG.34: 5 residues within 4Å: Chain A: N.763, I.1149 Chain B: T.949, S.950, A.951 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.949, B:A.951 NAG.35: 2 residues within 4Å: Chain A: R.1217, N.1231 No protein-ligand interaction detected (PLIP) NAG.38: 3 residues within 4Å: Chain B: V.28, N.198, T.200 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.28, B:N.198 NAG.39: 2 residues within 4Å: Chain B: N.282, Q.283 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Q.283 Hydrogen bonds: B:Q.283 NAG.40: 1 residues within 4Å: Chain B: N.649 No protein-ligand interaction detected (PLIP) NAG.41: 5 residues within 4Å: Chain B: N.763, I.1149 Chain C: T.949, S.950, A.951 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.949, C:A.951 NAG.42: 2 residues within 4Å: Chain B: R.1217, N.1231 No protein-ligand interaction detected (PLIP) NAG.45: 3 residues within 4Å: Chain C: V.28, N.198, T.200 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:V.28, C:N.198 NAG.46: 2 residues within 4Å: Chain C: N.282, Q.283 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Q.283 Hydrogen bonds: C:Q.283 NAG.47: 1 residues within 4Å: Chain C: N.649 No protein-ligand interaction detected (PLIP) NAG.48: 5 residues within 4Å: Chain A: T.949, S.950, A.951 Chain C: N.763, I.1149 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.949, A:A.951 NAG.49: 2 residues within 4Å: Chain C: R.1217, N.1231 No protein-ligand interaction detected (PLIP)

6 x PAM: PALMITOLEIC ACID(Non-covalent)

PAM.36: 14 residues within 4Å: Chain A: I.311, F.329, C.331, A.371, V.372, L.373, P.374, I.380, V.390, N.391, F.393, Y.395 Chain C: G.655, V.656 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.311, A:F.329, A:A.371, A:P.374, A:I.380, A:V.390, A:F.393, A:F.393, A:Y.395, A:Y.395, A:Y.395 Hydrogen bonds: A:N.391 PAM.37: 14 residues within 4Å: Chain A: F.466, S.685, Q.687, I.699, S.700, S.701, Y.733 Chain B: Q.820, A.823, R.824, Y.899, Y.916, L.923, P.924 12 PLIP interactions: 6 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:A.823, B:R.824, B:Y.899, B:L.923, B:P.924, A:F.466, A:Q.687, A:I.699, A:Y.733, A:Y.733 Salt bridges: B:R.824 Hydrogen bonds: A:F.466 PAM.43: 14 residues within 4Å: Chain A: G.655, V.656 Chain B: I.311, F.329, C.331, A.371, V.372, L.373, P.374, I.380, V.390, N.391, F.393, Y.395 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:I.311, B:F.329, B:A.371, B:P.374, B:I.380, B:V.390, B:F.393, B:F.393, B:Y.395, B:Y.395, B:Y.395 Hydrogen bonds: B:N.391 PAM.44: 14 residues within 4Å: Chain B: F.466, S.685, Q.687, I.699, S.700, S.701, Y.733 Chain C: Q.820, A.823, R.824, Y.899, Y.916, L.923, P.924 12 PLIP interactions: 6 interactions with chain B, 6 interactions with chain C Hydrophobic interactions: B:F.466, B:Q.687, B:I.699, B:Y.733, B:Y.733, C:A.823, C:R.824, C:Y.899, C:L.923, C:P.924 Hydrogen bonds: B:F.466 Salt bridges: C:R.824 PAM.50: 14 residues within 4Å: Chain B: G.655, V.656 Chain C: I.311, F.329, C.331, A.371, V.372, L.373, P.374, I.380, V.390, N.391, F.393, Y.395 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:I.311, C:F.329, C:A.371, C:P.374, C:I.380, C:V.390, C:F.393, C:F.393, C:Y.395, C:Y.395, C:Y.395 Hydrogen bonds: C:N.391 PAM.51: 14 residues within 4Å: Chain A: Q.820, A.823, R.824, Y.899, Y.916, L.923, P.924 Chain C: F.466, S.685, Q.687, I.699, S.700, S.701, Y.733 12 PLIP interactions: 6 interactions with chain C, 6 interactions with chain A Hydrophobic interactions: C:F.466, C:Q.687, C:I.699, C:Y.733, C:Y.733, A:A.823, A:R.824, A:Y.899, A:L.923, A:P.924 Hydrogen bonds: C:F.466 Salt bridges: A:R.824

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kirchdoerfer, R.N. et al., Structure and immune recognition of the porcine epidemic diarrhea virus spike protein. Structure (2021)

Release Date

2020-02-26

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein