SMTL ID : 1kae.1

L-HISTIDINOL DEHYDROGENASE (HISD) STRUCTURE COMPLEXED WITH L-HISTIDINOL (SUBSTRATE), ZINC AND NAD (COFACTOR)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 2 residues within 4Å: Chain A: S.81, D.82 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.82 Water bridges: A:E.83 SO4.2: 3 residues within 4Å: Chain A: P.249, R.280, R.287 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.287 Salt bridges: A:R.280 SO4.7: 3 residues within 4Å: Chain A: P.293 Chain B: R.415, T.417 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.417, B:T.417 Salt bridges: B:R.415 SO4.8: 2 residues within 4Å: Chain B: P.249, R.280 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.280

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: Q.259, H.262, D.360 Chain B: H.419 Ligands: HSO.5 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Metal complexes: A:H.262, A:D.360, B:H.419 ZN.9: 4 residues within 4Å: Chain A: H.419 Chain B: H.262, D.360 Ligands: IMD.10 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:H.262, B:D.360, A:H.419, H2O.17

1 x DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE(Non-covalent)

DTT.4: 3 residues within 4Å: Chain A: S.11, C.12, Q.16 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.16, A:Q.16

1 x HSO: L-histidinol(Non-covalent)

HSO.5: 15 residues within 4Å: Chain A: S.140, S.237, Q.259, H.262, E.326, H.327, E.356, D.360, Y.361, H.367 Chain B: E.414, L.416, H.419 Ligands: ZN.3, NAD.6 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:H.367 Hydrogen bonds: A:S.140, A:S.237, A:E.326, A:D.360, B:E.414

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

NAD.6: 16 residues within 4Å: Chain A: F.58, Y.130, P.132, G.133, T.141, P.162, G.185, G.186, Q.188, P.209, G.210, N.211, F.213, V.214, H.262 Ligands: HSO.5 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:H.262 Hydrogen bonds: A:G.133, A:T.141, A:T.141, A:Q.188, A:N.211, A:N.211, A:N.211 Water bridges: A:G.133, A:A.187 pi-Stacking: A:F.58, A:F.58, A:F.213 NAD.11: 14 residues within 4Å: Chain B: F.58, Y.130, P.132, G.133, P.162, G.185, G.186, Q.188, P.209, G.210, N.211, F.213, V.214, H.262 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:H.262 Hydrogen bonds: B:Y.130, B:Y.130, B:G.133, B:T.141, B:G.185, B:N.211, B:N.211 Water bridges: B:G.185 pi-Stacking: B:F.213

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.10: 9 residues within 4Å: Chain A: E.414, L.416, H.419 Chain B: S.140, H.262, D.360, Y.361, H.367 Ligands: ZN.9 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.140, A:E.414

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 3 residues within 4Å: Chain B: P.273, D.312, L.313 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.313 Water bridges: B:D.244, B:A.314

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Barbosa, J.A.R.G. et al., Mechanism of action and NAD+-binding mode revealed by the crystal structure of L-histidinol dehydrogenase. Proc.Natl.Acad.Sci.USA (2002)

Release Date

2002-06-12

Peptides

Histidinol dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Histidinol dehydrogenase

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