SMTL ID : 5vlb.1 (2 other biounits)

Crystal Structure of Medicago truncatula L-Histidinol Dehydrogenase in Complex with Imidazole

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.270, D.369 Chain B: H.428 Ligands: IMD.2 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:H.428, A:H.270, A:D.369, H2O.1, H2O.2 ZN.4: 4 residues within 4Å: Chain A: H.428 Chain B: H.270, D.369 Ligands: IMD.5 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:H.270, B:D.369, A:H.428, H2O.7, H2O.8

2 x IMD: IMIDAZOLE(Non-covalent)

IMD.2: 9 residues within 4Å: Chain A: S.144, H.270, D.369, Y.370, H.376 Chain B: E.423, L.425, H.428 Ligands: ZN.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.144 IMD.5: 10 residues within 4Å: Chain A: E.423, L.425, H.428 Chain B: L.142, S.144, H.270, D.369, Y.370, H.376 Ligands: ZN.4 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.144

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 5 residues within 4Å: Chain A: T.205, E.206, C.208, P.209, K.210 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.210, A:K.210 PEG.6: 5 residues within 4Å: Chain B: T.205, E.206, T.207, C.208, P.209 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.205 Water bridges: B:H.188

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ruszkowski, M. et al., Structures of Medicago truncatula L-Histidinol Dehydrogenase Show Rearrangements Required for NAD(+) Binding and the Cofactor Positioned to Accept a Hydride. Sci Rep (2017)

Release Date

2017-09-20

Peptides

Histidinol dehydrogenase, chloroplastic: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Histidinol dehydrogenase, chloroplastic

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