SMTL ID : 2zz3.1

Covalent complex of orotidine monophosphate decarboxylase D70A mutant from M. thermoautotrophicus with 6-cyano-UMP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x 6CN: 6-cyanouridine 5'-phosphate(Covalent)

6CN.1: 16 residues within 4Å: Chain A: A.21, D.23, K.45, K.75, L.126, M.129, S.130, P.183, V.185, Q.188, V.204, G.205, R.206 Chain B: D.78, I.79, T.82 17 PLIP interactions: 1 interactions with chain B, 16 interactions with chain A Hydrogen bonds: B:T.82, 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 Hydrophobic interactions: A:K.75, A:P.183 Water bridges: A:G.184, A:G.184, A:G.184, A:S.207 Salt bridges: A:R.206 6CN.5: 16 residues within 4Å: Chain A: D.78, I.79, T.82 Chain B: A.21, D.23, K.45, K.75, L.126, M.129, S.130, P.183, V.185, Q.188, V.204, G.205, R.206 19 PLIP interactions: 17 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:K.75, 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, A:T.82 Water bridges: B:D.23, 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 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.36, A:N.213 GOL.3: 3 residues within 4Å: Chain A: T.162, P.164, G.189 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.188 GOL.4: 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.6: 5 residues within 4Å: Chain B: A.211, D.212, N.213, A.216, A.217 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.212, B:N.213, B:N.213, B:A.216

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
B

Orotidine 5'-phosphate decarboxylase