SMTL ID : 3ex3.1

human orotidyl-5'-monophosphate decarboxylase in complex with 6-azido-UMP, covalent adduct

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-dimer

Ligands

2 x U5P: URIDINE-5'-MONOPHOSPHATE(Covalent)

U5P.1: 17 residues within 4Å: Chain A: S.37, D.39, K.61, H.63, D.92, K.94, 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: 16 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:P.197 Hydrogen bonds: A:S.37, A:K.61, A:D.92, A:K.94, A:S.152, A:S.152, A:S.152, A:Q.210, A:G.230, A:R.231, B:D.97, B:T.101 Water bridges: A:G.198, A:V.199, A:G.232, A:G.232 Salt bridges: A:R.231 U5P.3: 16 residues within 4Å: Chain A: D.97, I.98, T.101 Chain B: S.37, D.39, K.61, H.63, D.92, K.94, M.151, S.152, P.197, Q.210, Y.212, G.230, R.231 17 PLIP interactions: 15 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:P.197 Hydrogen bonds: B:S.37, B:K.61, B:D.92, B:K.94, 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:V.199, B:G.232 Salt bridges: B:R.231

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: K.22, I.79, A.82, K.83, F.87, L.88, D.118 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.22, A:A.82, A:K.83, A:K.83, A:F.87 Water bridges: A:D.118, A:R.143

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
B

Orotidine-5'-phosphate decarboxylase

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