SMTL ID : 8bj4.2 (1 other biounit)

Crystal structure of Medicago truncatula histidinol-phosphate aminotransferase (HISN6) in apo form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 8 residues within 4Å: Chain A: E.97, D.100, L.101, R.104, K.249, Q.250, N.253 Chain B: R.104 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:R.104, A:E.97, A:D.100, A:R.104, A:Q.250, A:N.253 EDO.2: 8 residues within 4Å: Chain A: T.119, F.120, T.121, N.169, P.170, Y.333, R.343 Ligands: SO4.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.121, A:T.121, A:N.169, A:Y.333 EDO.4: 7 residues within 4Å: Chain A: E.198, R.219, T.220, F.221, R.224, A.225, Y.234 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.198, A:R.224, A:R.224, A:Y.234, A:Y.234 Water bridges: A:R.219, A:A.225 EDO.5: 5 residues within 4Å: Chain A: R.283, G.284, F.287, P.300, S.301 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.283, A:S.301 Water bridges: A:V.280, A:G.284 EDO.6: 4 residues within 4Å: Chain A: I.174, I.175, D.176, D.179 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.176, A:D.179 Water bridges: A:L.145 EDO.14: 7 residues within 4Å: Chain B: D.81, E.198, R.219, T.220, R.224, A.225, Y.234 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.224, B:R.224, B:Y.234, B:Y.234 Water bridges: B:R.219, B:R.224 EDO.15: 8 residues within 4Å: Chain B: P.170, R.331, H.332, Y.333, L.338, Y.341, R.343 Ligands: EDO.17 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.333, B:Y.341, B:R.343 EDO.16: 5 residues within 4Å: Chain B: R.283, G.284, F.287, P.300, S.301 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.283, B:S.301 Water bridges: B:V.280, B:G.284 EDO.17: 9 residues within 4Å: Chain B: T.119, F.120, T.121, N.169, Y.333, L.338, R.343 Ligands: EDO.15, SO4.22 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.119, B:T.121, B:N.169, B:R.331 EDO.18: 3 residues within 4Å: Chain A: Y.17 Chain B: E.70, W.246 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.70, B:R.72 Water bridges: B:R.75 EDO.19: 5 residues within 4Å: Chain B: I.197, E.198, E.203, S.204, R.219 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.197, B:S.204 EDO.20: 7 residues within 4Å: Chain B: R.139, F.143, T.165, N.168, S.173, I.174, I.175 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.139, B:R.139, B:S.173

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

SO4.3: 3 residues within 4Å: Chain A: D.176, D.177, D.178 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.176, A:D.177, A:D.178 SO4.7: 4 residues within 4Å: Chain A: N.169, R.331, R.343 Ligands: EDO.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.169, A:N.169 Water bridges: A:N.43, A:N.43 Salt bridges: A:R.331, A:R.343 SO4.8: 7 residues within 4Å: Chain A: G.94, A.95, D.96, T.220, S.222, R.231 Chain B: Y.66 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:A.95, A:D.96, A:T.220, A:S.222, B:Y.66 Water bridges: A:D.96, B:Y.66, B:Y.66 Salt bridges: A:R.231 SO4.9: 4 residues within 4Å: Chain A: R.331, Y.333, S.334, N.335 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.334, A:S.334, A:N.335, A:N.335 Salt bridges: A:R.331 SO4.10: 2 residues within 4Å: Chain A: R.32, R.361 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.32, A:R.361, A:R.361 Salt bridges: A:R.32, A:R.361 SO4.11: 5 residues within 4Å: Chain A: P.69, W.246, K.249, P.251 Chain B: P.19 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.70 SO4.12: 5 residues within 4Å: Chain A: F.199, S.200, T.201, R.283, H.302 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.201, A:T.201 Water bridges: A:R.283 Salt bridges: A:R.283, A:H.302 SO4.21: 7 residues within 4Å: Chain A: Y.66 Chain B: G.94, A.95, D.96, T.220, S.222, R.231 10 PLIP interactions: 3 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:Y.66, B:A.95, B:D.96, B:S.222 Water bridges: A:Y.66, A:Y.66, B:D.96, B:K.223 Salt bridges: B:K.223, B:R.231 SO4.22: 6 residues within 4Å: Chain B: Y.17, F.120, N.169, R.331, R.343 Ligands: EDO.17 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:Y.17, B:N.169, B:N.169 Water bridges: B:Y.17, B:Y.17, B:N.43, B:N.43, B:R.331, B:R.331 Salt bridges: B:R.331, B:R.343 SO4.23: 5 residues within 4Å: Chain B: F.199, S.200, T.201, R.283, H.302 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.201, B:T.201 Salt bridges: B:R.283, B:H.302

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

NA.13: 3 residues within 4Å: Chain A: K.291, V.293, L.296 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.290 NA.24: 4 residues within 4Å: Chain B: L.290, K.291, V.293, L.296 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.290

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
C

B
D

histidinol-phosphate aminotransferase

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