SMTL ID : 3wk0.1

Wild-type orotidine 5'-monophosphate decarboxylase from M. thermoautotrophicus complexed with orotidine 5'-monophosphate methyl ester

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.41 Å

Oligo State

homo-dimer

Ligands

2 x O7M: 6-(methoxycarbonyl)uridine 5'-(dihydrogen phosphate)(Non-covalent)

O7M.1: 19 residues within 4Å: Chain A: A.21, D.23, K.45, D.73, K.75, I.99, L.126, M.129, S.130, V.158, P.183, V.185, Q.188, V.204, G.205, R.206 Chain B: D.78, I.79, T.82 23 PLIP interactions: 21 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:P.183 Hydrogen bonds: A:D.23, A:K.45, A:K.75, A:S.130, A:S.130, A:S.130, A:Q.188, A:G.205, A:R.206, B:T.82, B:T.82 Water bridges: A:D.23, A:D.73, A:D.73, A:G.184, A:G.184, A:G.184, A:G.184, A:S.207 Salt bridges: A:K.45, A:K.75, A:R.206 O7M.4: 19 residues within 4Å: Chain A: D.78, I.79, T.82 Chain B: A.21, D.23, K.45, D.73, K.75, I.99, L.126, M.129, S.130, V.158, P.183, V.185, Q.188, V.204, G.205, R.206 19 PLIP interactions: 18 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:S.130, B:Q.188, B:G.205, B:R.206, A:T.82 Water bridges: B:G.184, B:G.184, B:G.184, B:G.184, B:S.207 Salt bridges: B:K.45, B:K.75, B:R.206

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: E.36, N.213, A.215 3 PLIP interactions: 3 interactions with chain A Water bridges: A:E.36, A:D.212, A:N.213 GOL.3: 5 residues within 4Å: Chain A: A.211, D.212, N.213, A.216, A.217 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.212, A:N.213, A:A.216 GOL.5: 3 residues within 4Å: Chain B: E.36, N.213, A.215 3 PLIP interactions: 3 interactions with chain B Water bridges: B:E.36, B:D.212, B:N.213 GOL.6: 5 residues within 4Å: Chain B: A.211, D.212, N.213, A.216, A.217 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.212, B:N.213, B:A.216

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fujihashi, M. et al., Substrate distortion contributes to the catalysis of orotidine 5'-monophosphate decarboxylase. J.Am.Chem.Soc. (2013)

Release Date

2013-12-04

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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