SMTL ID : 8bj1.1

Crystal structure of Medicago truncatula histidinol-phosphate aminotransferase (HISN6) in the open state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.57 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: R.328, H.329, Y.330, S.331, N.332 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.329, A:S.331, A:N.332, A:N.332 Salt bridges: A:R.328 SO4.2: 5 residues within 4Å: Chain A: F.117, N.166, R.328, R.340 Ligands: EDO.8 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.166 Water bridges: A:D.38, A:R.328 Salt bridges: A:R.328, A:R.340 SO4.3: 5 residues within 4Å: Chain A: F.196, S.197, T.198, R.280, H.299 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.196, A:T.198 Water bridges: A:R.280 Salt bridges: A:R.280, A:H.299 SO4.12: 5 residues within 4Å: Chain B: F.196, S.197, T.198, R.280, H.299 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.198, B:T.198 Salt bridges: B:R.280, B:H.299 SO4.13: 5 residues within 4Å: Chain B: T.118, R.328, Y.330, S.331, N.332 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.331, B:N.332, B:N.332 Water bridges: B:R.328 Salt bridges: B:R.328 SO4.14: 5 residues within 4Å: Chain B: F.117, T.118, N.166, R.328, R.340 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.166, B:N.166 Water bridges: B:N.40, B:T.118, B:R.340, B:R.340 Salt bridges: B:R.328, B:R.340

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

EDO.4: 7 residues within 4Å: Chain A: E.195, R.216, T.217, F.218, R.221, A.222, Y.231 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.216, A:R.221, A:R.221, A:Y.231 Water bridges: A:R.216, A:R.221 EDO.5: 3 residues within 4Å: Chain A: Y.241, R.244 Chain B: R.9 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.9, A:R.244, A:R.244 EDO.6: 4 residues within 4Å: Chain A: E.67, W.243 Chain B: Y.14, P.16 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.72, A:R.72, A:R.72 EDO.7: 2 residues within 4Å: Chain A: F.292, L.359 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.315 EDO.8: 8 residues within 4Å: Chain A: T.116, F.117, T.118, N.166, P.167, Y.330, R.340 Ligands: SO4.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.118, A:T.118, A:N.166, A:N.166, A:Y.330, A:R.340 EDO.9: 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.10: 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:E.200 EDO.15: 7 residues within 4Å: Chain B: E.195, R.216, T.217, F.218, R.221, A.222, Y.231 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:E.195, B:R.216, B:R.221, B:R.221, B:Y.231, B:Y.231 Water bridges: B:R.216, B:A.222 EDO.16: 4 residues within 4Å: Chain A: Y.14, P.16 Chain B: E.67, W.243 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.69, B:R.72, B:R.72 EDO.17: 5 residues within 4Å: Chain B: R.280, G.281, F.284, P.297, S.298 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.280, B:S.298 EDO.18: 4 residues within 4Å: Chain B: I.194, E.195, E.200, S.201 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:I.194, B:S.201 Water bridges: B:E.200, B:E.200, B:R.221 EDO.19: 3 residues within 4Å: Chain B: L.178, W.205, H.209 No protein-ligand interaction detected (PLIP) EDO.20: 7 residues within 4Å: Chain A: Y.61, V.62 Chain B: F.20, P.31, E.32, I.34, K.36 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:Y.61, B:E.32 Water bridges: B:K.36, B:K.36, B:K.36 EDO.21: 4 residues within 4Å: Chain B: P.115, R.137, P.138, F.140 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.138 Water bridges: B:P.114 EDO.22: 3 residues within 4Å: Chain A: R.9 Chain B: Y.241, R.244 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.244, B:R.244

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

NA.11: 4 residues within 4Å: Chain A: L.287, K.288, V.290, L.293 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.287 NA.23: 4 residues within 4Å: Chain B: L.287, 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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