SMTL ID : 7qrf.1

Structure of the dimeric complex between precursor membrane ectodomain (prM) and envelope protein ectodomain (E) from tick-borne encephalitis virus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.28 Å

Oligo State

hetero-2-2-mer

Ligands

2 x UNK- UNK- UNK- UNK- UNK: Unknown peptide(Non-covalent)

UNK-UNK-UNK-UNK-UNK.1: 6 residues within 4Å: Chain B: A.1, T.2, V.3, Q.23, V.24, R.25 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:T.2, B:R.25 Hydrogen bonds: B:A.1, B:V.3, B:V.3, B:R.25 UNK-UNK-UNK-UNK-UNK.12: 6 residues within 4Å: Chain D: A.1, T.2, V.3, Q.23, V.24, R.25 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:T.2, D:R.25 Hydrogen bonds: D:A.1, D:V.3, D:V.3, D:Q.23, D:R.25

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: T.60, R.61, R.221, H.233 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.61 Salt bridges: A:R.61, A:R.221, A:H.233 SO4.13: 4 residues within 4Å: Chain C: T.60, R.61, R.221, H.233 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.61 Salt bridges: C:R.61, C:R.221, C:H.233

2 x PE4: 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL(Non-functional Binders)

PE4.3: 9 residues within 4Å: Chain A: W.223, D.226, L.227, A.228, L.229, Q.264, V.267, A.271 Chain C: K.270 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:K.270, C:K.270 Water bridges: A:A.228, A:A.228 PE4.14: 9 residues within 4Å: Chain A: K.270 Chain C: W.223, D.226, L.227, A.228, L.229, Q.264, V.267, A.271 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:K.270, A:K.270, C:D.226 Water bridges: C:A.228, C:A.228

16 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 2 residues within 4Å: Chain A: K.97, F.248 Ligand excluded by PLIP EDO.5: 2 residues within 4Å: Chain A: G.92, N.238 Ligand excluded by PLIP EDO.6: 4 residues within 4Å: Chain A: G.249, A.250, Y.259 Chain C: V.277 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain A: E.62, K.130, K.232, E.234, G.235 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: F.15, H.327, T.329, I.362, Q.379 Ligand excluded by PLIP EDO.9: 3 residues within 4Å: Chain A: D.355, V.356, N.357 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: H.252 Chain B: D.61, V.62, D.63 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain B: A.1, T.2, E.16, K.18, D.19 Ligand excluded by PLIP EDO.15: 2 residues within 4Å: Chain C: K.97, F.248 Ligand excluded by PLIP EDO.16: 2 residues within 4Å: Chain C: G.92, N.238 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain A: V.277 Chain C: G.249, A.250, Y.259 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain C: E.62, K.130, K.232, E.234, G.235 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain C: F.15, H.327, T.329, I.362, Q.379 Ligand excluded by PLIP EDO.20: 3 residues within 4Å: Chain C: D.355, V.356, N.357 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain C: H.252 Chain D: D.61, V.62, D.63 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain D: A.1, T.2, E.16, K.18, D.19 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vaney, M.C. et al., Evolution and activation mechanism of the flavivirus class II membrane-fusion machinery. Nat Commun (2022)

Release Date

2022-05-25

Peptides

Envelope protein E: AC
Genome polyprotein: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
D

D
D

Envelope protein E

Genome polyprotein

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