SMTL ID : 3sm8.1

Crystal Structure of Pseudomonas aeruginosa D-Arginine Dehydrogenase in Complex with an (N5) Flavin Adduct

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.07 Å

Oligo State

monomer

Ligands

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: G.217, V.218, R.219, A.325, N.326 Ligands: GOL.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.217, A:R.219, A:N.326 Water bridges: A:A.325 GOL.2: 7 residues within 4Å: Chain A: W.187, A.216, G.217, N.326, A.327, E.328 Ligands: GOL.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.217, A:E.328 Water bridges: A:N.326 GOL.3: 6 residues within 4Å: Chain A: P.267, N.269, D.271, L.283, D.284, T.287 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.284 Water bridges: A:S.253, A:P.267, A:P.267, A:A.270, A:D.271

1 x FNK: [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-5-[7,8-dimethyl-5-(3-methylbutanoyl)-2,4-dioxo-1,3,4,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate(Non-covalent)

FNK.4: 39 residues within 4Å: Chain A: I.15, G.16, G.18, I.19, A.20, L.37, E.38, R.39, E.40, P.43, H.46, S.47, T.48, R.50, S.51, A.52, A.53, H.54, T.56, Y.59, E.176, A.177, A.204, A.205, G.206, W.208, I.212, R.228, M.246, Y.255, G.309, R.311, Q.336, G.337, G.338, Y.339, G.340, I.341, Q.342 38 PLIP interactions: 38 interactions with chain A Hydrophobic interactions: A:A.52, A:Y.59, A:R.228, A:Y.255, A:R.311 Hydrogen bonds: A:G.18, A:A.20, A:R.39, A:R.39, A:R.39, A:E.40, A:S.47, A:T.48, A:T.48, A:A.52, A:H.54, A:H.54, A:E.176, A:A.177, A:A.177, A:G.206, A:R.228, A:G.337, A:Y.339, A:G.340, A:I.341, A:Q.342 Water bridges: A:G.21, A:H.46, A:H.46, A:H.46, A:H.46, A:Y.59, A:A.204, A:A.207, A:Q.336 pi-Cation interactions: A:R.39, A:R.311

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fu, G. et al., Atomic-resolution structure of an N5 flavin adduct in D-arginine dehydrogenase. Biochemistry (2011)

Release Date

2011-07-20

Peptides

FAD-dependent catabolic D-arginine dehydrogenase, DauA: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

FAD-dependent catabolic D-arginine dehydrogenase, DauA

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