SMTL ID : 6p9d.1

Crystal Structure of Pseudomonas aeruginosa D-Arginine Dehydrogenase Y249F variant with FAD - Yellow fraction

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.33 Å

Oligo State

monomer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 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:Y.20, A:N.161 Water bridges: A:W.21 GOL.2: 7 residues within 4Å: Chain A: Y.20, P.73, A.74, G.75, F.76, G.157, R.160 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.20, A:Y.20, A:R.160 Water bridges: A:G.75, A:G.153 GOL.3: 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, A:H.299 GOL.4: 5 residues within 4Å: Chain A: A.210, G.211, V.212, N.320, A.321 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.320

1 x FDA: DIHYDROFLAVINE-ADENINE DINUCLEOTIDE(Non-covalent)

FDA.5: 36 residues within 4Å: Chain A: I.9, G.10, G.12, I.13, A.14, L.31, E.32, R.33, E.34, P.37, 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, G.303, R.305, Q.330, G.331, G.332, Y.333, G.334, I.335, Q.336 39 PLIP interactions: 39 interactions with chain A Hydrophobic interactions: A:A.46, A:R.222, A:R.305 Hydrogen bonds: A:G.12, A:A.14, A:R.33, A:R.33, A:P.37, A:H.40, A:S.41, A:T.42, A:T.42, A:S.45, A:S.45, A:S.45, A:A.46, A:A.47, A:H.48, A:H.48, A:A.171, A:A.171, A:G.331, A:Y.333, A:G.334, A:I.335, A:Q.336, A:Q.336 Water bridges: A:G.15, A:R.33, A:R.33, A:H.40, A:H.40, A:H.40, A:H.40, A:H.40, A:E.170, A:G.200, A:A.201 pi-Cation interactions: A:R.33

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Iyer, A. et al., A Single-Point Mutation in d-Arginine Dehydrogenase Unlocks a Transient Conformational State Resulting in Altered Cofactor Reactivity. Biochemistry (2021)

Release Date

2020-06-17

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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