SMTL ID : 3abi.1

Crystal Structure of L-Lysine Dehydrogenase from Hyperthermophilic Archaeon Pyrococcus horikoshii

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.44 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 8 residues within 4Å: Chain A: V.159, G.160, G.161, Y.172, W.176, E.184, T.240, R.242 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.159, A:G.161, A:W.176 Salt bridges: A:R.242 SO4.3: 4 residues within 4Å: Chain B: E.79, K.101, V.102, D.103 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.101, B:D.103 Water bridges: B:E.79, B:D.103

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

NAD.2: 29 residues within 4Å: Chain A: G.23, A.24, G.25, N.26, I.27, D.45, V.46, N.50, V.63, D.64, A.65, S.66, A.84, L.85, P.86, G.87, L.89, V.107, S.108, F.109, G.133, F.134, A.135, P.136, W.176, S.177, D.180, M.311, T.315 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:W.176, A:T.315 Hydrogen bonds: A:A.24, A:A.24, A:N.26, A:I.27, A:V.46, A:D.64, A:A.65, A:S.66, A:L.85, A:F.109, A:G.133, A:F.134, A:A.135, A:P.136, A:S.177, A:D.180, A:D.180 Water bridges: A:G.28 NAD.4: 26 residues within 4Å: Chain B: A.24, G.25, N.26, I.27, G.28, D.45, V.46, N.47, N.50, V.63, D.64, A.65, S.66, A.84, L.85, P.86, G.87, L.89, V.107, S.108, F.109, G.133, F.134, A.135, P.136, T.315 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:I.27, B:T.315 Hydrogen bonds: B:A.24, B:A.24, B:N.26, B:I.27, B:G.28, B:V.46, B:D.64, B:A.65, B:S.66, B:L.85, B:F.109, B:F.134, B:A.135, B:P.136

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yoneda, K. et al., First crystal structure of L-lysine 6-dehydrogenase as an NAD-dependent amine dehydrogenase. J.Biol.Chem. (2010)

Release Date

2009-12-29

Peptides

Putative uncharacterized protein PH1688: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Putative uncharacterized protein PH1688