SMTL ID : 3n2m.1

Crystal structure of Plasmodium falciparum orotidine 5'-monophosphate decarboxylase complexed with 5-fluoro-6-amino-UMP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x FNU: 6-amino-5-fluorouridine 5'-(dihydrogen phosphate)(Non-covalent)

FNU.1: 19 residues within 4Å: Chain A: D.42, K.121, N.123, D.155, K.157, L.210, T.213, T.214, V.259, P.283, I.285, Q.288, N.310, I.311, G.312, R.313 Chain B: D.160, I.161, T.164 20 PLIP interactions: 2 interactions with chain B, 18 interactions with chain A Hydrogen bonds: B:D.160, B:T.164, A:D.42, A:K.121, A:N.123, A:D.155, A:K.157, A:T.214, A:T.214, A:T.214, A:Q.288, A:N.310, A:G.312, A:R.313 Water bridges: A:N.123, A:G.284, A:G.284, A:G.284, A:A.287 Salt bridges: A:R.313 FNU.4: 19 residues within 4Å: Chain A: D.160, I.161, T.164 Chain B: D.42, K.121, N.123, D.155, K.157, L.210, T.213, T.214, V.259, P.283, A.287, Q.288, N.310, I.311, G.312, R.313 20 PLIP interactions: 19 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.42, B:K.121, B:N.123, B:D.155, B:D.155, B:K.157, B:T.214, B:T.214, B:I.285, B:Q.288, B:G.312, B:R.313, A:D.160 Water bridges: B:N.123, B:G.284, B:G.284, B:G.284, B:A.287, B:N.310 Salt bridges: B:R.313

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.2: 7 residues within 4Å: Chain A: M.20, G.21, F.22, D.179, Y.204, Y.205, E.254 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.204, A:E.254 Water bridges: A:Y.204

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

PEG.3: 4 residues within 4Å: Chain A: N.318, M.327, Y.328, Q.331 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.318, A:Q.331

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 6 residues within 4Å: Chain B: K.166, R.169, Y.197, D.198, E.199, E.200 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.198, B:E.199, B:E.200 Water bridges: B:R.169, B:D.194 Salt bridges: B:K.166, B:R.169

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

EDO.6: 6 residues within 4Å: Chain A: N.215, P.216 Chain B: I.161, G.162, N.190, M.191 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Water bridges: A:N.215, A:D.217, B:N.190 Hydrogen bonds: B:G.162

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, Y. et al., Crystal structure of Plasmodium falciparum orotidine 5'-monophosphate decarboxylase complexed with 5-fluoro-6-amino-UMP. To be Published

Release Date

2011-04-06

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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