SMTL ID : 2zz1.1

Snapshot of the reaction from 6-CN-UMP to BMP catalyzed by Orotidine Monophosphate Deacarboxylase from M. thermoautotrophicum

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.57 Å

Oligo State

homo-dimer

Ligands

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

BMP.1: 17 residues within 4Å: Chain A: A.21, D.23, K.45, D.73, K.75, M.129, S.130, P.183, V.185, Q.188, V.204, G.205, R.206 Chain B: D.78, I.79, T.82 Ligands: 6CN.2 19 PLIP interactions: 18 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:P.183 Hydrogen bonds: A:D.23, A:K.45, A:D.73, A:K.75, A:S.130, A:S.130, A:S.130, A:V.185, A:Q.188, A:G.205, A:R.206, B:T.82 Water bridges: A:G.184, A:G.184, A:G.184, A:G.184, A:S.207 Salt bridges: A:R.206 BMP.6: 17 residues within 4Å: Chain A: D.78, I.79, T.82 Chain B: A.21, D.23, K.45, D.73, K.75, M.129, S.130, P.183, V.185, Q.188, V.204, G.205, R.206 Ligands: 6CN.7 23 PLIP interactions: 21 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:P.183 Hydrogen bonds: B:D.23, B:K.45, B:D.73, B:K.75, B:S.130, B:S.130, B:S.130, B:V.185, B:Q.188, B:G.205, B:R.206, A:T.82, A:T.82 Water bridges: B:D.23, B:D.73, B:D.73, B:G.184, B:G.184, B:G.184, B:G.184, B:S.207 Salt bridges: B:R.206

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

6CN.2: 18 residues within 4Å: Chain A: A.21, D.23, K.45, D.73, K.75, I.99, M.129, S.130, P.183, V.185, Q.188, V.204, G.205, R.206 Chain B: D.78, I.79, T.82 Ligands: BMP.1 17 PLIP interactions: 16 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:P.183 Hydrogen bonds: 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, B:T.82 Water bridges: A:G.184, A:G.184, A:G.184, A:G.184, A:S.207 Salt bridges: A:R.206 6CN.7: 18 residues within 4Å: Chain A: D.78, I.79, T.82 Chain B: A.21, D.23, K.45, D.73, K.75, I.99, M.129, S.130, P.183, V.185, Q.188, V.204, G.205, R.206 Ligands: BMP.6 22 PLIP interactions: 20 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:P.183 Hydrogen bonds: B:D.23, B:K.45, B:K.75, B:S.130, B:S.130, B:S.130, B:V.185, B:Q.188, B:G.205, B:R.206, A:T.82, A:T.82 Water bridges: B:D.23, B:D.73, B:D.73, 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.3: 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.4: 3 residues within 4Å: Chain A: T.162, P.164, G.189 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.188 GOL.5: 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.8: 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

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