SMTL ID : 4nuw.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.59 Å

Oligo State

homo-dimer

Ligands

2 x U5P: URIDINE-5'-MONOPHOSPHATE(Non-covalent)

U5P.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: 17 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:P.180 Hydrogen bonds: A:D.20, 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 Water bridges: A:G.181, A:G.181, A:G.181, A:G.181, A:S.204 Salt bridges: A:R.203 U5P.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 19 PLIP interactions: 17 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:P.180 Hydrogen bonds: B:D.20, 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 Water bridges: B:G.181, B:G.181, B:G.181, B:G.181, B:S.204, A:E.78 Salt bridges: B:R.203

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: E.33, N.210, A.212 4 PLIP interactions: 4 interactions with chain A Water bridges: A:E.33, A:E.33, A:E.33, A:N.210

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

EDO.3: 2 residues within 4Å: Chain A: Q.185, R.203 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.203, A:R.203 EDO.4: 4 residues within 4Å: Chain A: A.103, D.104, R.107, L.149 3 PLIP interactions: 3 interactions with chain A Water bridges: A:D.104, A:R.107, A:R.107

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 uridine 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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