SMTL ID : 3pby.1

Crystal structure of the mutant L123S of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with 6-azauridine 5'-monophosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-dimer

Ligands

2 x UP6: 6-AZA URIDINE 5'-MONOPHOSPHATE(Non-covalent)

UP6.1: 16 residues within 4Å: Chain A: A.18, D.20, K.42, D.70, K.72, M.126, S.127, P.180, V.182, Q.185, V.201, G.202, R.203 Chain B: D.75, I.76, T.79 17 PLIP interactions: 15 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.42, A:K.72, A:S.127, A:V.182, A:Q.185, A:G.202, A:R.203, B:D.75, B:T.79 Water bridges: A:K.72, A:G.181, A:G.181, A:G.181, A:G.181, A:S.204, A:Y.206 Salt bridges: A:R.203 UP6.3: 16 residues within 4Å: Chain A: D.75, I.76, T.79 Chain B: A.18, D.20, K.42, D.70, K.72, M.126, S.127, P.180, V.182, Q.185, V.201, G.202, R.203 20 PLIP interactions: 3 interactions with chain A, 17 interactions with chain B Hydrogen bonds: A:D.75, A:T.79, A:T.79, B:K.42, B:K.72, B:S.127, B:V.182, B:Q.185, B:G.202, B:R.203 Water bridges: B:D.70, B:D.70, B:K.72, B:G.181, B:G.181, B:G.181, B:G.181, B:S.204, B:Y.206 Salt bridges: B:R.203

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: E.33, N.210, A.212 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.33, A:N.210

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Iiams, V. et al., Mechanism of the orotidine 5'-monophosphate decarboxylase-catalyzed reaction: importance of residues in the orotate binding site. Biochemistry (2011)

Release Date

2011-09-21

Peptides

Orotidine 5'-monophosphate decarboxylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Orotidine 5'-monophosphate decarboxylase

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