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

Crystal Structure of Medicago truncatula L-Histidinol Dehydrogenase in Complex with L-Histidine and NAD+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.59 Å

Oligo State

homo-dimer

Ligands

2 x HIS: HISTIDINE(Non-covalent)

HIS.1: 16 residues within 4Å: Chain A: L.142, S.144, S.245, Q.267, H.270, E.335, H.336, E.365, D.369, Y.370, H.376 Chain B: E.423, L.425, H.428 Ligands: NAD.2, ZN.5 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:H.376 Hydrogen bonds: A:S.144, A:S.245, A:D.369, A:D.369, B:E.423 Salt bridges: A:H.336, A:H.376 pi-Cation interactions: A:H.270 HIS.6: 16 residues within 4Å: Chain A: E.423, L.425, H.428 Chain B: L.142, S.144, S.245, Q.267, H.270, E.335, H.336, E.365, D.369, Y.370, H.376 Ligands: ZN.3, NAD.7 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.144, B:S.245, B:E.365, B:D.369, B:D.369, A:E.423 Salt bridges: B:H.336, B:H.376

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.2: 30 residues within 4Å: Chain A: I.41, F.64, D.65, Y.134, P.136, G.137, G.138, T.139, A.140, L.142, P.166, G.193, G.194, Q.196, P.217, G.218, N.219, Y.221, V.222, A.242, G.243, P.244, S.245, H.270, E.335, H.376, V.377, L.378, T.380 Ligands: HIS.1 19 PLIP interactions: 18 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:P.217, A:P.217, H.1 Hydrogen bonds: A:D.65, A:G.137, A:G.138, A:T.139, A:A.140, A:Q.196, A:N.219, A:N.219, A:S.245, A:H.270, A:S.274, A:L.378, A:L.378 pi-Stacking: A:F.64, A:F.64, A:Y.221 NAD.7: 28 residues within 4Å: Chain B: F.64, D.65, Y.134, P.136, G.137, G.138, T.139, L.142, P.166, G.193, G.194, Q.196, P.217, G.218, N.219, Y.221, V.222, A.242, G.243, P.244, S.245, H.270, E.335, H.376, V.377, L.378, T.380 Ligands: HIS.6 19 PLIP interactions: 18 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:P.217, H.6 Hydrogen bonds: B:D.65, B:Y.134, B:Y.134, B:G.137, B:G.138, B:T.139, B:A.140, B:Q.196, B:N.219, B:N.219, B:Y.221, B:S.245, B:S.274, B:E.335, B:L.378, B:L.378 pi-Stacking: B:Y.221

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: H.428 Chain B: Q.267, H.270, D.369 Ligands: HIS.6 4 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions, 1 interactions with chain A Metal complexes: B:H.270, B:D.369, HIS.6, A:H.428 ZN.5: 5 residues within 4Å: Chain A: Q.267, H.270, D.369 Chain B: H.428 Ligands: HIS.1 4 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: B:H.428, A:H.270, A:D.369, HIS.1

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

PEG.4: 3 residues within 4Å: Chain A: Q.59, Y.60, K.63 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.59

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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