SMTL ID : 4o11.1

Crystal structure of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with 6-hydroxyuridine 5'-monophosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.59 Å

Oligo State

homo-dimer

Ligands

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

BMP.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 19 PLIP interactions: 18 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:P.180 Hydrogen bonds: A:D.20, A:K.42, A:D.70, 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:T.79 Water bridges: A:G.181, A:G.181, A:G.181, A:G.181, A:S.204 Salt bridges: A:R.203 BMP.7: 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 21 PLIP interactions: 20 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:P.180 Hydrogen bonds: B:D.20, B:K.42, B:D.70, 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: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 Salt bridges: B:R.203

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

CL.2: 3 residues within 4Å: Chain A: I.76, P.77, E.78 Ligand excluded by PLIP CL.3: 4 residues within 4Å: Chain A: A.103, D.104 Chain B: G.130, M.133 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain A: G.130, M.133 Chain B: A.103, D.104 Ligands: GOL.9 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: E.33, N.210, A.212 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.210 GOL.9: 5 residues within 4Å: Chain B: A.103, D.104, R.107, L.149 Ligands: CL.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.107

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

EDO.5: 5 residues within 4Å: Chain A: A.208, D.209, N.210, A.213, A.214 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.209, A:N.210, A:N.210 EDO.6: 4 residues within 4Å: Chain A: Y.37, N.210, A.212, A.213 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.37, A:N.210

1 x MG: MAGNESIUM ION(Non-covalent)

MG.10: 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.11, H2O.11, H2O.13, H2O.14, 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-hydroxyuridine 5'-monophosphate. To be Published

Release Date

2014-01-15

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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