SMTL ID : 5kcy.1

Crystal structure of the aromatic prenyltransferase AtaPT from Aspergillus terreus A8-4 in complex with geranyl S-thiolodiphosphate and (+)-butyrolactone II

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

4 x XBU: methyl (2~{R})-3-(4-hydroxyphenyl)-2-[(4-hydroxyphenyl)methyl]-4-oxidanyl-5-oxidanylidene-furan-2-carboxylate(Non-covalent)

XBU.1: 11 residues within 4Å: Chain A: H.83, E.86, S.172, Y.185, S.187, L.247, A.265, L.318, R.391, W.392 Ligands: GST.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.247 Hydrogen bonds: A:S.172, A:S.172, A:R.391, A:R.391 Salt bridges: A:R.391 pi-Stacking: A:H.83, A:Y.185 XBU.3: 9 residues within 4Å: Chain B: H.83, E.86, C.170, S.172, L.318, P.319, R.391, W.392 Ligands: GST.4 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:P.319 Hydrogen bonds: B:R.391, B:R.391 Water bridges: B:H.83 Salt bridges: B:H.83, B:R.391 pi-Stacking: B:H.83 XBU.5: 11 residues within 4Å: Chain C: H.83, E.86, S.172, Y.185, S.187, L.247, A.265, L.318, R.391, W.392 Ligands: GST.6 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:L.247 Hydrogen bonds: C:S.172, C:S.172, C:R.391, C:R.391 Salt bridges: C:R.391 pi-Stacking: C:H.83, C:Y.185 XBU.7: 9 residues within 4Å: Chain D: H.83, E.86, C.170, S.172, L.318, P.319, R.391, W.392 Ligands: GST.8 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:P.319 Hydrogen bonds: D:R.391, D:R.391 Water bridges: D:H.83 Salt bridges: D:H.83, D:R.391 pi-Stacking: D:H.83

4 x GST: GERANYL S-THIOLODIPHOSPHATE(Non-covalent)

GST.2: 18 residues within 4Å: Chain A: K.90, R.99, K.183, Y.185, R.259, K.261, Y.263, L.264, A.265, P.319, F.320, G.321, N.323, Q.337, Y.339, W.392, Y.408 Ligands: XBU.1 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:Y.263, A:Y.263, A:A.265, A:P.319, A:Y.339, A:Y.339, A:W.392, A:Y.408 Hydrogen bonds: A:R.99, A:N.323, A:Q.337, A:Q.337, A:Y.339, A:Y.408 Salt bridges: A:K.90, A:R.99, A:R.259, A:K.261 GST.4: 16 residues within 4Å: Chain B: K.90, R.99, K.183, Y.185, R.259, K.261, Y.263, L.264, F.320, G.321, N.323, Q.337, Y.339, W.392, Y.408 Ligands: XBU.3 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:Y.263, B:Y.263, B:Y.263, B:Y.339, B:W.392, B:W.392, B:Y.408 Hydrogen bonds: B:R.99, B:R.99, B:K.183, B:K.183, B:Y.185, B:Y.263, B:N.323, B:Q.337, B:Q.337, B:Y.339 Salt bridges: B:K.90, B:R.99, B:K.183, B:R.259, B:K.261 GST.6: 18 residues within 4Å: Chain C: K.90, R.99, K.183, Y.185, R.259, K.261, Y.263, L.264, A.265, P.319, F.320, G.321, N.323, Q.337, Y.339, W.392, Y.408 Ligands: XBU.5 18 PLIP interactions: 18 interactions with chain C Hydrophobic interactions: C:Y.263, C:Y.263, C:A.265, C:P.319, C:Y.339, C:Y.339, C:W.392, C:Y.408 Hydrogen bonds: C:R.99, C:N.323, C:Q.337, C:Q.337, C:Y.339, C:Y.408 Salt bridges: C:K.90, C:R.99, C:R.259, C:K.261 GST.8: 16 residues within 4Å: Chain D: K.90, R.99, K.183, Y.185, R.259, K.261, Y.263, L.264, F.320, G.321, N.323, Q.337, Y.339, W.392, Y.408 Ligands: XBU.7 22 PLIP interactions: 22 interactions with chain D Hydrophobic interactions: D:Y.263, D:Y.263, D:Y.263, D:Y.339, D:W.392, D:W.392, D:Y.408 Hydrogen bonds: D:R.99, D:R.99, D:K.183, D:K.183, D:Y.185, D:Y.263, D:N.323, D:Q.337, D:Q.337, D:Y.339 Salt bridges: D:K.90, D:R.99, D:K.183, D:R.259, D:K.261

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, R. et al., Molecular insights into the enzyme promiscuity of an aromatic prenyltransferase. Nat. Chem. Biol. (2017)

Release Date

2016-12-21

Peptides

aromatic prenyltransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

aromatic prenyltransferase

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