SMTL ID : 3w07.1

Atomic resolution structure of orotidine 5'-monophosphate decarboxylase from Methanothermobacter thermoautotrophicus bound with UMP.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.03 Å

Oligo State

homo-dimer

Ligands

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

U5P.1: 19 residues within 4Å: Chain A: A.21, D.23, K.45, D.73, K.75, L.126, M.129, S.130, P.183, G.184, V.185, Q.188, I.203, V.204, G.205, R.206 Chain B: D.78, I.79, T.82 19 PLIP interactions: 2 interactions with chain B, 17 interactions with chain A Hydrogen bonds: B:D.78, B:T.82, A:D.23, A:K.45, A:K.75, A:S.130, A:S.130, A:S.130, A:V.185, A:Q.188, A:G.205, A:R.206 Hydrophobic interactions: A:P.183 Water bridges: A:D.23, A:G.184, A:G.184, A:G.184, A:S.207 Salt bridges: A:R.206 U5P.3: 19 residues within 4Å: Chain A: D.78, I.79, T.82 Chain B: A.21, D.23, K.45, D.73, K.75, L.126, M.129, S.130, P.183, G.184, V.185, Q.188, I.203, V.204, G.205, R.206 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:P.183 Hydrogen bonds: B:D.23, B:K.45, B:K.75, B:S.130, B:S.130, B:V.185, B:Q.188, B:G.205, B:R.206, A:D.78 Water bridges: B:G.184, B:G.184, B:G.184, B:S.207 Salt bridges: B:R.206

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: E.36, N.213, P.214, A.215 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.36, A:N.213 GOL.4: 4 residues within 4Å: Chain B: E.36, N.213, P.214, A.215 2 PLIP interactions: 2 interactions with chain B Water bridges: B:E.36, B:N.213

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fujihashi, M. et al., Atomic resolution structure of the orotidine 5'-monophosphate decarboxylase product complex combined with surface plasmon resonance analysis: implications for the catalytic mechanism. J.Biol.Chem. (2013)

Release Date

2013-02-20

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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