SMTL ID : 5wan.1

Crystal Structure of a flavoenzyme RutA in the pyrimidine catabolic pathway

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x URA: URACIL(Non-covalent)

URA.1: 6 residues within 4Å: Chain A: F.41, W.49, M.83, W.96, F.242 Ligands: FMN.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.49 URA.10: 6 residues within 4Å: Chain B: F.41, W.49, M.83, W.96, F.242 Ligands: FMN.18 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.49

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 3 residues within 4Å: Chain A: K.260, P.357, G.358 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.358 Water bridges: A:A.359, A:E.360 Salt bridges: A:K.260 SO4.3: 3 residues within 4Å: Chain A: A.55, P.56, Q.57 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.57, A:Q.57 SO4.4: 3 residues within 4Å: Chain A: K.66, Q.70, V.112 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.70 Water bridges: A:Q.70 Salt bridges: A:K.66 SO4.5: 3 residues within 4Å: Chain A: T.329, S.330, A.331 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.330, A:A.331 Water bridges: A:T.329 SO4.11: 3 residues within 4Å: Chain B: K.260, P.357, G.358 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.358 Water bridges: B:A.359 Salt bridges: B:K.260 SO4.12: 3 residues within 4Å: Chain B: A.55, P.56, Q.57 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.57, B:Q.57 SO4.13: 3 residues within 4Å: Chain B: K.66, Q.70, V.112 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.70 Water bridges: B:Q.70 Salt bridges: B:K.66 SO4.14: 3 residues within 4Å: Chain B: T.329, S.330, A.331 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.330, B:A.331 Water bridges: B:T.329

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain A: Y.58, D.368, F.369, L.370 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.58, A:F.369, A:L.370 GOL.7: 4 residues within 4Å: Chain A: R.187, D.188, G.191, T.192 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.187, A:D.188 Water bridges: A:D.188 GOL.8: 5 residues within 4Å: Chain A: N.46, N.47, Y.58, M.59, T.93 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.46, A:T.93 Water bridges: A:M.59 GOL.15: 4 residues within 4Å: Chain B: Y.58, D.368, F.369, L.370 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.58, B:F.369, B:L.370 GOL.16: 4 residues within 4Å: Chain B: R.187, D.188, G.191, T.192 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.187 Water bridges: B:D.188 GOL.17: 5 residues within 4Å: Chain B: N.46, N.47, Y.58, M.59, T.93 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.46, B:T.93 Water bridges: B:M.59

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.9: 17 residues within 4Å: Chain A: F.41, M.83, I.84, T.121, V.152, G.154, R.175, Y.176, A.222, G.223, Q.224, S.225, G.228, F.240, F.242, L.363 Ligands: URA.1 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:F.41, A:A.222, A:F.242, A:L.363 Hydrogen bonds: A:I.84, A:I.84, A:G.154, A:R.175, A:Q.224, A:S.225, A:G.228 Water bridges: A:N.150, A:N.150, A:T.153, A:T.153, A:T.153, A:G.154, A:W.155 Salt bridges: A:R.175 FMN.18: 17 residues within 4Å: Chain B: F.41, M.83, I.84, T.121, V.152, G.154, R.175, Y.176, A.222, G.223, Q.224, S.225, G.228, F.240, F.242, L.363 Ligands: URA.10 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:F.41, B:A.222, B:F.242, B:L.363 Hydrogen bonds: B:I.84, B:I.84, B:T.121, B:G.154, B:R.175, B:Y.176, B:Q.224, B:S.225, B:G.228 Water bridges: B:N.150, B:N.150, B:T.153, B:T.153, B:T.153, B:G.154, B:W.155 Salt bridges: B:R.175

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mukherjee, T. et al., Catalysis of a flavoenzyme-mediated amide hydrolysis. J. Am. Chem. Soc. (2010)

Release Date

2017-07-19

Peptides

Pyrimidine monooxygenase RutA: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Pyrimidine monooxygenase RutA