SMTL ID : 7kv8.1 (3 other biounits)

Chimeric flavivirus between Binjari virus and Dengue virus serotype-2

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: N.149, N.153, G.156, H.158 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.153 NAG.2: 3 residues within 4Å: Chain A: N.67, F.90, M.118 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.90 Hydrogen bonds: A:N.67 NAG.5: 6 residues within 4Å: Chain B: N.149, N.153, T.155, G.156, H.158 Chain C: G.102 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.153 NAG.6: 4 residues within 4Å: Chain B: N.67, R.89, F.90, M.118 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.90 Hydrogen bonds: B:N.67 NAG.9: 6 residues within 4Å: Chain B: G.102 Chain C: N.149, N.153, T.155, G.156, H.158 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.153, C:G.156 NAG.10: 3 residues within 4Å: Chain C: N.67, F.90, M.118 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.90 Hydrogen bonds: C:N.67

3 x 6OU: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate(Non-covalent)

6OU.3: 8 residues within 4Å: Chain A: T.404, T.405, G.408, A.409, R.411, M.412, F.422, G.423 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.405, A:A.409 Salt bridges: A:R.411 6OU.7: 9 residues within 4Å: Chain B: F.11, V.12, T.404, T.405, G.408, A.409, R.411, M.412, F.422 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.409 Hydrogen bonds: B:F.11 Salt bridges: B:R.411 6OU.11: 7 residues within 4Å: Chain C: T.404, T.405, G.408, A.409, R.411, M.412, G.423 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:T.405, C:A.409 Water bridges: C:E.13 Salt bridges: C:R.411

3 x 1Q0: (2S,3R,4Z)-3-hydroxy-2-[(9E)-octadec-9-enoylamino]octadec-4-en-1-yl dihydrogen phosphate(Non-covalent)

1Q0.4: 13 residues within 4Å: Chain A: A.409, M.412, A.413, I.414, L.415, G.416, W.420, G.433, H.437, G.441, Y.444, Y.488, L.489 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:A.409, A:M.412, A:W.420, A:W.420, A:H.437, A:Y.444, A:Y.488, A:Y.488, A:L.489 Hydrogen bonds: A:A.413 1Q0.8: 15 residues within 4Å: Chain B: A.409, M.412, A.413, I.414, L.415, G.416, W.420, G.433, H.437, F.440, G.441, Y.444, V.484, Y.488, L.489 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:A.409, B:W.420, B:H.437, B:Y.444, B:Y.444, B:Y.488, B:Y.488, B:Y.488, B:L.489 Hydrogen bonds: B:A.413 1Q0.12: 15 residues within 4Å: Chain C: A.409, M.412, A.413, I.414, G.416, W.420, G.433, L.436, H.437, G.441, Y.444, V.484, V.485, Y.488, L.489 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:M.412, C:W.420, C:W.420, C:L.436, C:H.437, C:Y.444, C:Y.444, C:V.484, C:V.485, C:Y.488, C:Y.488, C:L.489 Hydrogen bonds: C:A.413

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hardy, J.M. et al., A unified route for flavivirus structures uncovers essential pocket factors conserved across pathogenic viruses. Nat Commun (2021)

Release Date

2020-12-23

Peptides

Envelope protein E: ABC
Matrix protein M: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
a

E
b

F
c

Envelope protein E

Matrix protein M

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