SMTL ID : 4nx5.1

Crystal structure of orotidine 5'-monophosphate decarboxylase from methanobacterium thermoautotrophicum complexed with 6-azauridine 5'-monophosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.59 Å

Oligo State

homo-dimer

Ligands

2 x UP6: 6-AZA URIDINE 5'-MONOPHOSPHATE(Non-covalent)

UP6.1: 16 residues within 4Å: Chain A: A.18, D.20, K.42, D.70, K.72, M.126, S.127, P.180, V.182, Q.185, V.201, G.202, R.203 Chain B: D.75, I.76, T.79 18 PLIP interactions: 16 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.42, A:K.72, A:S.127, A:S.127, A:S.127, A:V.182, A:Q.185, A:G.202, A:R.203, B:D.75, B:T.79 Water bridges: A:G.181, A:G.181, A:G.181, A:G.181, A:S.204, A:Y.206 Salt bridges: A:R.203 UP6.5: 16 residues within 4Å: Chain A: D.75, I.76, T.79 Chain B: A.18, D.20, K.42, D.70, K.72, M.126, S.127, P.180, V.182, Q.185, V.201, G.202, R.203 20 PLIP interactions: 18 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.42, B:K.72, B:S.127, B:S.127, B:S.127, B:V.182, B:Q.185, B:G.202, B:R.203, A:D.75, A:T.79 Water bridges: B:D.70, B:D.70, B:G.181, B:G.181, B:G.181, B:G.181, B:S.204, B:Y.206 Salt bridges: B:R.203

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

CL.2: 3 residues within 4Å: Chain A: A.103, D.104 Chain B: G.130 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain A: I.76, P.77, E.78 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: G.130 Chain B: A.103, D.104 Ligands: GOL.9 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain B: I.76, P.77, E.78 Ligand excluded by PLIP

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 4 residues within 4Å: Chain A: D.140, R.144, R.166, I.170 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.144, A:R.144, A:R.166 Water bridges: A:D.140

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 3 residues within 4Å: Chain B: T.159, P.161, G.186 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.186 GOL.9: 5 residues within 4Å: Chain B: A.103, D.104, R.107, L.149 Ligands: CL.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.107

2 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.11: 1 residues within 4Å: Chain B: S.221 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:S.221, H2O.10, H2O.11, H2O.12, H2O.17, H2O.17

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fedorov, A.A. et al., Crystal structure of orotidine 5'-monophosphate decarboxylase from methanobacterium thermoautotrophicum complexed with 6-azauridine 5'-monophosphate. To be Published

Release Date

2013-12-25

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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