SMTL ID : 3g1h.2 (6 other biounits)

Crystal structure of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with 5,6-dihydrouridine 5'-monophosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x H2U: 5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE(Non-covalent)

H2U.1: 16 residues within 4Å: Chain A: A.18, D.20, K.42, D.70, K.72, L.123, M.126, S.127, P.180, Q.185, V.201, G.202, R.203 Chain B: D.75, I.76, T.79 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.123 Hydrogen bonds: A:D.20, A:D.20, A:K.42, A:K.72, A:S.127, A:S.127, A:S.127, A:Q.185, A:G.202, A:R.203, B:T.79, B:T.79 Salt bridges: A:R.203 H2U.2: 15 residues within 4Å: Chain A: D.75, I.76, T.79 Chain B: D.20, K.42, D.70, K.72, M.126, S.127, P.180, V.182, Q.185, V.201, G.202, R.203 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.20, B:K.42, B:K.72, B:S.127, B:S.127, B:S.127, B:V.182, B:Q.185, B:G.202, B:R.203, A:T.79 Water bridges: B:A.184, B:S.204 Salt bridges: B:R.203

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chan, K.K. et al., Mechanism of the orotidine 5'-monophosphate decarboxylase-catalyzed reaction: evidence for substrate destabilization. Biochemistry (2009)

Release Date

2009-06-23

Peptides

Orotidine 5'-phosphate decarboxylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Orotidine 5'-phosphate decarboxylase

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