SMTL ID : 2zz7.1

Orotidine Monophosphate Decarboxylase K72A mutant complexed with BMP (produced from 6-Iodo-UMP)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.58 Å

Oligo State

homo-dimer

Ligands

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

BMP.1: 15 residues within 4Å: Chain A: A.21, D.23, K.45, D.73, M.129, S.130, P.183, V.185, Q.188, V.204, G.205, R.206 Chain B: D.78, I.79, T.82 22 PLIP interactions: 20 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:P.183 Hydrogen bonds: A:D.23, A:K.45, A:D.73, A:S.130, A:S.130, A:S.130, A:V.185, 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:R.206 BMP.4: 15 residues within 4Å: Chain A: D.78, I.79, T.82 Chain B: A.21, D.23, K.45, D.73, M.129, S.130, P.183, V.185, Q.188, V.204, G.205, R.206 18 PLIP interactions: 17 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:P.183 Hydrogen bonds: B:D.23, B:K.45, B:D.73, B:S.130, B:S.130, B:S.130, B:V.185, 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: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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.212, A:N.213 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 Water bridges: B:D.212

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fujihashi, M. et al., Structural characterization of the molecular events during a slow substrate-product transition in orotidine 5'-monophosphate decarboxylase. J.Mol.Biol. (2009)

Release Date

2009-03-24

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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