SMTL ID : 8bj3.1

Crystal structure of Medicago truncatula histidinol-phosphate aminotransferase (HISN6) in complex with histidinol-phosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.61 Å

Oligo State

homo-dimer

Ligands

2 x QNX: [(2~{S})-3-(1~{H}-imidazol-4-yl)-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]propyl] dihydrogen phosphate(Non-covalent)(Covalent)

QNX.1: 21 residues within 4Å: Chain A: Y.14, G.91, A.92, D.93, I.96, F.117, T.118, M.119, T.162, N.166, D.190, A.192, Y.193, T.217, S.219, K.220, R.228, R.328, R.340 Chain B: Y.63, Y.249 25 PLIP interactions: 22 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.117, A:T.162, A:A.192, A:Y.193, B:Y.63 Hydrogen bonds: A:Y.14, A:A.92, A:D.93, A:D.93, A:N.166, A:Y.193, A:Y.193, A:S.219, A:K.220, B:Y.63 Water bridges: A:R.340, A:R.340, A:R.340 Salt bridges: A:K.220, A:R.228, A:R.328, A:R.340 pi-Stacking: A:F.117, A:F.117, B:Y.249 QNX.7: 21 residues within 4Å: Chain A: Y.63, Y.249 Chain B: Y.14, G.91, A.92, D.93, I.96, F.117, T.118, M.119, T.162, N.166, D.190, A.192, Y.193, T.217, S.219, K.220, R.228, R.328, R.340 22 PLIP interactions: 19 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.117, B:T.162, B:Y.193, A:Y.63 Hydrogen bonds: B:Y.14, B:A.92, B:D.93, B:D.93, B:N.166, B:Y.193, B:Y.193, B:T.217, B:S.219 Water bridges: B:R.340, A:Y.249 Salt bridges: B:K.220, B:R.228, B:R.328, B:R.340 pi-Stacking: B:F.117, B:F.117, A:Y.249

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

EDO.2: 5 residues within 4Å: Chain A: R.280, G.281, F.284, P.297, S.298 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.280, A:S.298 Water bridges: A:V.277, A:G.281 EDO.3: 2 residues within 4Å: Chain A: E.67, W.243 3 PLIP interactions: 3 interactions with chain A Water bridges: A:E.67, A:R.72, A:R.72 EDO.4: 3 residues within 4Å: Chain A: F.292, V.311, L.359 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.315 EDO.5: 4 residues within 4Å: Chain A: I.194, E.195, E.200, S.201 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.194, A:S.201 Water bridges: A:R.216 EDO.8: 2 residues within 4Å: Chain B: E.67, W.243 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.67 Water bridges: B:R.72, B:R.72 EDO.9: 5 residues within 4Å: Chain B: R.280, G.281, F.284, P.297, S.298 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.280, B:S.298 Water bridges: B:V.277, B:G.281 EDO.10: 8 residues within 4Å: Chain A: R.101 Chain B: E.94, D.97, L.98, R.101, K.246, Q.247, N.250 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:R.101, B:E.94, B:D.97, B:D.97, B:R.101, B:Q.247, B:N.250

2 x NA: SODIUM ION(Non-functional Binders)

NA.6: 3 residues within 4Å: Chain A: K.288, V.290, L.293 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.293 NA.11: 3 residues within 4Å: Chain B: K.288, V.290, L.293 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.288

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rutkiewicz, M. et al., Insights into the substrate specificity, structure, and dynamics of plant histidinol-phosphate aminotransferase (HISN6). Plant Physiol Biochem. (2023)

Release Date

2023-03-22

Peptides

histidinol-phosphate aminotransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

histidinol-phosphate aminotransferase

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