SMTL ID : 2q8z.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: R.169, E.174, D.198, K.201 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.174 Water bridges: A:R.169, A:R.169, A:R.169 Salt bridges: A:R.169, A:K.201 SO4.5: 6 residues within 4Å: Chain B: K.166, R.169, Y.197, D.198, E.199, E.200 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:D.198, B:E.199, B:E.200, B:E.200 Water bridges: B:D.194, B:D.194 Salt bridges: B:K.166, B:R.169

2 x NUP: 6-AMINOURIDINE 5'-MONOPHOSPHATE(Non-covalent)

NUP.2: 18 residues within 4Å: Chain A: D.42, K.121, N.123, D.155, K.157, T.213, T.214, P.283, I.285, A.287, Q.288, N.310, I.311, G.312, R.313 Chain B: D.160, I.161, T.164 23 PLIP interactions: 21 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:P.283 Hydrogen bonds: 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, B:D.160, B:T.164 Water bridges: A:D.42, A:N.123, A:G.284, A:G.284, A:I.285, A:A.287, A:A.287 Salt bridges: A:R.313 NUP.6: 17 residues within 4Å: Chain A: D.160, I.161, T.164 Chain B: D.42, K.121, N.123, D.155, K.157, T.213, T.214, P.283, I.285, Q.288, N.310, I.311, G.312, R.313 21 PLIP interactions: 20 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:P.283 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:Q.288, B:G.312, B:R.313, A:D.160 Water bridges: B:N.123, B:G.284, B:G.284, B:A.287, B:A.287, B:A.287, B:N.310 Salt bridges: B:R.313

1 x 7PE: 2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL(Non-functional Binders)

7PE.3: 3 residues within 4Å: Chain A: M.327, Y.328, Q.331 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.331

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

PEG.4: 3 residues within 4Å: Chain A: Y.197, Y.204, Y.246 No protein-ligand interaction detected (PLIP) PEG.7: 5 residues within 4Å: Chain B: N.318, P.319, Y.320, K.323, A.324 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.318

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bello, A.M. et al., Structure-Activity Relationships of C6-Uridine Derivatives Targeting Plasmodia Orotidine Monophosphate Decarboxylase. J.Med.Chem. (2008)

Release Date

2008-01-29

Peptides

Orotidine-monophosphate-decarboxylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Orotidine-monophosphate-decarboxylase

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