SMTL ID : 6pld.1

Crystal Structure of Pseudomonas aeruginosa D-Arginine Dehydrogenase Y249F variant with 6-OH-FAD - Green fraction

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

monomer

Ligands

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

6FA.1: 38 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, F.249, G.303, L.304, R.305, Q.330, G.331, G.332, Y.333, G.334, I.335, Q.336 34 PLIP interactions: 34 interactions with chain A Hydrophobic interactions: 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:A.46, A:H.48, A:H.48, A:A.171, A:A.171, 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:H.40, A:G.200, A:A.201, A:Q.330 pi-Cation interactions: A:R.33, A:R.305

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

PEG.2: 6 residues within 4Å: Chain A: Y.20, W.21, S.23, A.24, P.73, N.161 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.161

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: E.34, A.35, Q.36, Y.39 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.34, A:E.34, A:A.35, A:Q.36, A:Q.36 GOL.4: 4 residues within 4Å: Chain A: G.43, S.45, H.299, W.301 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.45 GOL.5: 6 residues within 4Å: Chain A: F.92, S.93, S.243, D.245, S.247, L.285 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.243, A:S.243, A:S.247 Water bridges: A:L.244, A:E.288 GOL.6: 3 residues within 4Å: Chain A: L.115, D.117, Q.120 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.117, A:Q.120, A:Q.120 Water bridges: A:D.117 GOL.7: 4 residues within 4Å: Chain A: E.246, S.247, P.261, A.262 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.246, A:E.246 Water bridges: A:R.222 GOL.8: 4 residues within 4Å: Chain A: K.220, F.307, V.308, G.311 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.220, A:V.308

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

2020-07-01

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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