SMTL ID : 3ewy.1

K314A mutant of human orotidyl-5'-monophosphate decarboxylase soaked with OMP, decarboxylated to UMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.10 Å

Oligo State

homo-dimer

Ligands

2 x U5P: URIDINE-5'-MONOPHOSPHATE(Non-covalent)

U5P.1: 16 residues within 4Å: Chain A: S.37, D.39, K.61, H.63, D.92, M.151, S.152, P.197, Q.210, Y.212, V.229, G.230, R.231 Chain B: D.97, I.98, T.101 18 PLIP interactions: 15 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:P.197 Hydrogen bonds: A:S.37, A:D.39, A:K.61, A:S.152, A:S.152, A:S.152, A:Q.210, A:Y.212, A:G.230, A:R.231, B:D.97, B:T.101, B:T.101 Water bridges: A:G.198, A:G.198, A:Q.200 Salt bridges: A:R.231 U5P.4: 16 residues within 4Å: Chain A: D.97, I.98, T.101 Chain B: S.37, D.39, K.61, H.63, D.92, M.151, S.152, P.197, Q.210, Y.212, V.229, G.230, R.231 15 PLIP interactions: 13 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:P.197 Hydrogen bonds: B:S.37, B:K.61, B:S.152, B:S.152, B:S.152, B:Q.210, B:G.230, B:R.231, A:D.97, A:T.101 Water bridges: B:G.198, B:G.198, B:Q.200 Salt bridges: B:R.231

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: L.201, E.202, A.203 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.201, A:A.203 Water bridges: A:S.214, A:S.214 GOL.3: 7 residues within 4Å: Chain A: K.22, I.79, A.82, K.83, F.87, L.88, D.118 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.22, A:I.79, A:F.87, A:D.118 GOL.5: 3 residues within 4Å: Chain B: L.201, E.202, A.203 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.201, B:A.203 Water bridges: B:E.202, B:S.214, B:S.214 GOL.6: 7 residues within 4Å: Chain B: K.22, I.79, A.82, K.83, F.87, L.88, D.118 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.22, B:I.79, B:F.87, B:D.118 Water bridges: B:D.118

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Heinrich, D. et al., Lys314 is a nucleophile in non-classical reactions of orotidine-5'-monophosphate decarboxylase. Chemistry (2009)

Release Date

2009-04-07

Peptides

Orotidine-5'-phosphate decarboxylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Orotidine-5'-phosphate decarboxylase

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