SMTL ID : 8j1g.1 (1 other biounit)

Structure of amino acid dehydrogenase in complex with NADPH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.1: 24 residues within 4Å: Chain A: R.111, T.112, I.134, G.135, S.136, G.137, K.138, V.139, S.160, P.161, S.162, C.200, T.201, S.202, S.203, V.207, I.222, S.223, T.224, N.225, S.296, I.297, G.298 Ligands: ARG.2 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:T.112 Hydrogen bonds: A:R.111, A:S.136, A:G.137, A:K.138, A:V.139, A:S.160, A:S.160, A:S.162, A:S.162, A:S.202, A:S.202, A:S.203, A:S.203, A:S.203, A:I.222, A:T.224, A:N.225 Salt bridges: A:K.138, A:K.138 NDP.4: 24 residues within 4Å: Chain B: R.111, T.112, I.134, G.135, S.136, G.137, K.138, V.139, S.160, P.161, S.162, C.200, T.201, S.202, S.203, V.207, I.222, S.223, T.224, N.225, S.296, I.297, G.298 Ligands: ARG.5 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:T.112 Hydrogen bonds: B:R.111, B:S.136, B:G.137, B:K.138, B:V.139, B:S.160, B:S.160, B:S.162, B:S.162, B:S.202, B:S.202, B:S.203, B:S.203, B:I.222, B:T.224, B:N.225, B:N.225 Salt bridges: B:K.138, B:K.138

2 x ARG: ARGININE(Non-covalent)

ARG.2: 14 residues within 4Å: Chain A: D.54, F.55, I.56, Y.58, K.71, S.73, P.74, Y.75, V.84, T.108, R.111, T.224, N.225 Ligands: NDP.1 12 PLIP interactions: 10 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:V.84 Hydrogen bonds: A:I.56, A:S.73, A:S.73, A:Y.75, A:T.224, A:N.225, R.2, R.2 Salt bridges: A:D.54, A:K.71, A:R.111 ARG.5: 13 residues within 4Å: Chain B: D.54, F.55, I.56, Y.58, K.71, S.73, P.74, Y.75, V.84, T.108, R.111, T.224 Ligands: NDP.4 13 PLIP interactions: 2 Ligand-Ligand interactions, 11 interactions with chain B Hydrogen bonds: R.5, R.5, B:I.56, B:S.73, B:S.73, B:Y.75, B:T.224, B:T.224 Hydrophobic interactions: B:V.84 Water bridges: B:D.54 Salt bridges: B:D.54, B:K.71, B:R.111

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

EDO.3: 8 residues within 4Å: Chain A: Q.40, P.41, Q.43, Y.58, T.249, I.297, G.298, L.299 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.40, A:P.41, A:Q.43, A:Q.43, A:T.249 EDO.6: 9 residues within 4Å: Chain B: Q.40, P.41, A.42, Q.43, Y.58, T.249, G.298, L.299, G.300 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.40, B:P.41, B:Q.43, B:T.249 Water bridges: B:Q.43, B:Q.43

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kawakami, R. et al., First crystal structure of an NADP + -dependent l-arginine dehydrogenase belonging to the mu-crystallin family. Int.J.Biol.Macromol. (2023)

Release Date

2023-08-16

Peptides

Ornithine cyclodeaminase family protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ornithine cyclodeaminase family protein

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