SMTL ID : 2cze.1

Crystal structure of orotidine 5'-phosphate decarboxylase from Pyrococcus horikoshii OT3 complexed with UMP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

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

U5P.1: 18 residues within 4Å: Chain A: A.5, D.7, K.29, N.31, D.57, K.59, M.108, S.109, I.137, P.162, I.164, Q.167, V.184, G.185, R.186 Chain B: D.62, I.63, T.66 18 PLIP interactions: 15 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:P.162 Hydrogen bonds: A:K.29, A:N.31, A:S.109, A:S.109, A:S.109, A:Q.167, A:G.185, A:R.186, B:D.62, B:T.66, B:T.66 Water bridges: A:G.163, A:G.163, A:G.163, A:G.163, A:A.187 Salt bridges: A:R.186 U5P.4: 19 residues within 4Å: Chain A: D.62, I.63, T.66 Chain B: A.5, D.7, K.29, N.31, D.57, K.59, M.108, S.109, I.137, P.162, I.164, Q.167, I.183, V.184, G.185, R.186 20 PLIP interactions: 18 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:P.162 Hydrogen bonds: B:K.29, B:N.31, B:S.109, B:S.109, B:S.109, B:I.164, B:Q.167, B:G.185, B:R.186, A:D.62, A:T.66 Water bridges: B:D.7, B:G.163, B:G.163, B:G.163, B:G.163, B:A.187, B:Y.189 Salt bridges: B:R.186

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.2: 3 residues within 4Å: Chain A: R.68, L.69, R.72 7 PLIP interactions: 7 interactions with chain A Water bridges: A:R.68, A:R.72, A:R.72 Salt bridges: A:R.68, A:R.68, A:R.72, A:R.72

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 2 residues within 4Å: Chain A: E.98, L.99 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.98 Water bridges: A:L.99

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arai, R. et al., Crystal structure of orotidine 5'-phosphate decarboxylase from Pyrococcus horikoshii OT3 complexed with UMP. To be Published

Release Date

2006-01-13

Peptides

Orotidine 5'-phosphate decarboxylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Orotidine 5'-phosphate decarboxylase

Related Entries With Identical Sequence