SMTL ID : 4nt0.1

Crystal structure of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with 3-deazauridine 5'-monophosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

homo-dimer

Ligands

2 x 3DU: 4-hydroxy-1-(5-O-phosphono-beta-D-ribofuranosyl)pyridin-2(1H)-one(Non-covalent)

3DU.1: 13 residues within 4Å: Chain A: A.18, D.20, K.42, D.70, K.72, M.126, S.127, P.180, G.202, R.203 Chain B: D.75, I.76, T.79 17 PLIP interactions: 15 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:P.180, A:P.180 Hydrogen bonds: A:D.20, A:K.42, A:K.72, A:S.127, A:G.202, A:R.203, B:T.79, B:T.79 Water bridges: A:D.20, A:E.125, A:R.203, A:R.203, A:S.204, A:Y.206 Salt bridges: A:R.203 3DU.4: 13 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, G.202, R.203 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:P.180, B:P.180 Hydrogen bonds: B:D.20, B:K.42, B:K.72, B:S.127, B:G.202, B:R.203, A:T.79 Water bridges: B:E.125, B:R.203, B:R.203, B:R.203, B:S.204 Salt bridges: B:R.203

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: R.5, V.6, V.8, M.9, D.10 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:R.5, A:V.8, A:D.10, H2O.2, H2O.3 CA.5: 5 residues within 4Å: Chain B: R.5, V.6, V.8, M.9, D.10 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:R.5, B:V.8, B:D.10, H2O.6, H2O.6

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 6 residues within 4Å: Chain A: G.52, M.53, D.54 Chain B: G.52, M.53, D.54 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:D.54, B:D.54, A:M.53, A:D.54, A:D.54 Water bridges: B:M.53, B:M.53

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 3-deazauridine 5'-monophosphate. To be Published

Release Date

2013-12-18

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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