SMTL ID : 7rdf.1

Crystal structure of Pseudomonas aeruginosa D-Arginine Dehydrogenase Y249F co-crystallized in the presence of D-arginine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.29 Å

Oligo State

monomer

Ligands

1 x 4R2: [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{S})-5-[5-[(~{E})-4-carbamimidamidobut-2-enoyl]-7,8-dimethyl-2,4-bis(oxidanylidene)-1~{H}-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] hydrogen phosphate(Non-covalent)

4R2.1: 42 residues within 4Å: Chain A: I.9, G.10, G.12, I.13, A.14, L.31, E.32, R.33, E.34, H.40, S.41, T.42, R.44, S.45, A.46, A.47, H.48, T.50, Y.53, E.87, H.169, E.170, A.171, A.198, A.199, G.200, W.202, I.206, R.222, V.242, E.246, F.249, G.303, R.305, Q.330, G.331, G.332, Y.333, G.334, I.335, Q.336 Ligands: 6FA.2 42 PLIP interactions: 42 interactions with chain A Hydrophobic interactions: A:Y.53, A:R.222, A:R.305 Hydrogen bonds: A:G.12, A:A.14, A:R.33, A:R.33, A:R.33, A:E.34, A:S.41, A:S.41, A:T.42, A:T.42, A:A.46, A:H.48, A:T.50, A:A.171, A:A.171, A:R.222, A:Q.330, A:G.331, A:Y.333, A:G.334, A:I.335, A:Q.336 Water bridges: A:G.15, A:R.33, A:R.33, A:H.40, A:H.40, A:H.40, A:Y.53, A:E.87, A:E.170, A:G.200, A:A.201, A:E.246 Salt bridges: A:E.87, A:E.246 pi-Cation interactions: A:R.33, A:Y.53, A:R.305

1 x 6FA: 6-HYDROXY-FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

6FA.2: 38 residues within 4Å: Chain A: I.9, G.10, G.12, I.13, A.14, L.31, E.32, R.33, E.34, H.40, S.41, T.42, R.44, S.45, A.46, A.47, H.48, H.169, E.170, A.171, A.198, A.199, G.200, W.202, I.206, R.222, F.249, G.303, L.304, R.305, Q.330, G.331, G.332, Y.333, G.334, I.335, Q.336 Ligands: 4R2.1 34 PLIP interactions: 34 interactions with chain A Hydrophobic interactions: A:R.222, A:R.222, A:R.305 Hydrogen bonds: A:G.12, A:A.14, A:R.33, A:R.33, A:H.40, A:S.41, A:S.41, A:T.42, A:T.42, A:A.46, A:H.48, A:E.170, A:A.171, A:A.171, A:G.200, A:G.331, A:G.334, A:I.335, A:Q.336, A:Q.336 Water bridges: A:R.33, A:R.33, A:R.33, A:H.40, A:H.40, A:H.40, A:H.40, A:A.201, A:Q.330 pi-Cation interactions: A:R.33, A:R.305

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 1 residues within 4Å: Chain A: A.108 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.107 GOL.4: 6 residues within 4Å: Chain A: Y.20, W.21, S.23, A.24, P.73, N.161 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.23, A:A.24, A:N.161 GOL.5: 4 residues within 4Å: Chain A: E.34, A.35, Q.36, Y.39 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.35, A:Q.36

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

PEG.6: 5 residues within 4Å: Chain A: G.43, R.44, S.45, H.299, W.301 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.45 Water bridges: A:S.45

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Iyer, A. et al., Discovery of a new flavin N5-adduct in a tyrosine to phenylalanine variant of d-Arginine dehydrogenase. Arch.Biochem.Biophys. (2021)

Release Date

2021-12-22

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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