SMTL ID : 3qf0.1

Crystal structure of the mutant T159V,Y206F of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with the inhibitor BMP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.34 Å

Oligo State

homo-dimer

Ligands

2 x BMP: 6-HYDROXYURIDINE-5'-PHOSPHATE(Non-covalent)

BMP.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 18 PLIP interactions: 17 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:P.180 Hydrogen bonds: A:D.20, A:K.42, A:D.70, A:K.72, A:S.127, A:S.127, A:S.127, A:V.182, A:Q.185, A:G.202, A:R.203, B:T.79 Water bridges: A:G.181, A:G.181, A:G.181, A:S.204 Salt bridges: A:R.203 BMP.2: 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: 19 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:P.180 Hydrogen bonds: B:D.20, B:K.42, B:D.70, 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:D.70, B:D.70, B:G.181, B:G.181, B:G.181, B:S.204 Salt bridges: B:R.203

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: E.51, G.52 Chain B: G.52, M.53, D.54 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Water bridges: A:V.48, A:G.52, A:M.53, A:M.53, A:D.54, B:G.52 Hydrogen bonds: B:M.53, B:D.54, B:D.54

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Desai, B.J. et al., Conformational changes in orotidine 5'-monophosphate decarboxylase: a structure-based explanation for how the 5'-phosphate group activates the enzyme. Biochemistry (2012)

Release Date

2012-01-25

Peptides

Orotidine 5'-phosphate decarboxylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Orotidine 5'-phosphate decarboxylase