SMTL ID : 3wjz.1

Orotidine 5'-monophosphate decarboxylase D75N mutant from M. thermoautotrophicus complexed with 6-amino-UMP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.39 Å

Oligo State

homo-dimer

Ligands

2 x NUP: 6-AMINOURIDINE 5'-MONOPHOSPHATE(Non-covalent)

NUP.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: N.78, I.79, T.82 Ligands: CL.2 22 PLIP interactions: 19 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:P.183 Hydrogen bonds: A:D.23, A:K.45, A:D.73, A:K.75, A:K.75, A:S.130, A:S.130, A:S.130, A:Q.188, A:G.205, A:R.206, B:N.78, B:N.78, B:T.82 Water bridges: A:D.23, A:G.184, A:G.184, A:G.184, A:G.184, A:S.207 Salt bridges: A:R.206 NUP.5: 17 residues within 4Å: Chain A: N.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: CL.6 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:K.75, B:K.75, B:S.130, B:S.130, B:S.130, B:Q.188, B:G.205, B:R.206, A:N.78 Water bridges: B:G.184, B:G.184, B:G.184, B:G.184, B:S.207 Salt bridges: B:R.206

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 5 residues within 4Å: Chain A: K.75, M.129 Chain B: N.78, I.79 Ligands: NUP.1 Ligand excluded by PLIP CL.6: 5 residues within 4Å: Chain A: N.78, I.79 Chain B: K.75, M.129 Ligands: NUP.5 Ligand excluded by PLIP

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: E.36, N.213, A.215 3 PLIP interactions: 3 interactions with chain A Water bridges: A:D.212, A:N.213, A:N.213 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.7: 3 residues within 4Å: Chain B: E.36, N.213, A.215 3 PLIP interactions: 3 interactions with chain B Water bridges: B:D.212, B:N.213, B:N.213 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:A.216 Water bridges: B:D.212

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fujihashi, M. et al., Substrate distortion contributes to the catalysis of orotidine 5'-monophosphate decarboxylase. J.Am.Chem.Soc. (2013)

Release Date

2013-12-04

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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