SMTL ID : 3bje.1

Crystal structure of Trypanosoma brucei nucleoside phosphorylase shows uridine phosphorylase activity

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.44 Å

Oligo State

homo-dimer

Ligands

2 x R1P: 1-O-phosphono-alpha-D-ribofuranose(Non-covalent)

R1P.1: 14 residues within 4Å: Chain A: G.50, D.51, R.54, M.95, R.145, G.147, T.148, F.250, E.292, M.293, E.294 Chain B: H.34, R.74 Ligands: URA.2 13 PLIP interactions: 5 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:H.34, A:G.50, A:T.148, A:T.148, A:T.148, A:M.293 Water bridges: B:R.74, B:R.74 Salt bridges: B:R.74, B:R.74, A:R.54, A:R.145, A:R.145 R1P.3: 14 residues within 4Å: Chain A: H.34, R.74 Chain B: G.50, D.51, R.54, M.95, R.145, G.147, T.148, F.250, E.292, M.293, E.294 Ligands: URA.4 13 PLIP interactions: 9 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:G.50, B:D.51, B:T.148, B:T.148, B:M.293, A:H.34 Water bridges: B:T.148, A:R.74 Salt bridges: B:R.54, B:R.145, B:R.145, A:R.74, A:R.74

2 x URA: URACIL(Non-covalent)

URA.2: 12 residues within 4Å: Chain A: T.148, C.149, G.150, F.250, Q.254, R.256, I.291, E.292, M.293, V.316, S.317 Ligands: R1P.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.316 Hydrogen bonds: A:T.148, A:G.150, A:Q.254, A:Q.254, A:R.256, A:R.256, A:S.317 URA.4: 12 residues within 4Å: Chain B: T.148, C.149, G.150, F.250, Q.254, R.256, I.291, E.292, M.293, V.316, S.317 Ligands: R1P.3 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.250, B:V.316 Hydrogen bonds: B:T.148, B:G.150, B:Q.254, B:Q.254, B:R.256, B:R.256, B:S.317 Water bridges: B:T.148

1 x CA: CALCIUM ION(Non-covalent)

CA.5: 6 residues within 4Å: Chain A: M.95, D.98, N.99 Chain B: M.95, D.98, N.99 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Metal complexes: B:M.95, B:D.98, A:M.95, A:D.98, A:D.98

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Larson, E.T. et al., The Crystal Structure and Activity of a Putative Trypanosomal Nucleoside Phosphorylase Reveal It to be a Homodimeric Uridine Phosphorylase. J.Mol.Biol. (2010)

Release Date

2007-12-18

Peptides

Nucleoside phosphorylase, putative: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nucleoside phosphorylase, putative