SMTL ID : 3p0e.2 (2 other biounits)

Structure of hUPP2 in an active conformation with bound 5-benzylacyclouridine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x BAU: 1-((2-HYDROXYETHOXY)METHYL)-5-BENZYLPYRIMIDINE-2,4(1H,3H)-DIONE(Non-covalent)

BAU.1: 17 residues within 4Å: Chain A: M.99, T.130, S.131, G.132, F.202, Q.206, R.208, I.236, E.237, M.238, L.262, D.268, I.270 Chain B: Y.24, H.25, R.83 Ligands: PO4.2 10 PLIP interactions: 2 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:H.25, A:G.132, A:Q.206, A:Q.206, A:R.208, A:R.208 pi-Stacking: B:Y.24, A:F.202 Hydrophobic interactions: A:I.270 Water bridges: A:R.127 BAU.3: 17 residues within 4Å: Chain A: Y.24, H.25 Chain B: M.99, T.130, S.131, G.132, F.202, Q.206, R.208, I.236, E.237, M.238, L.261, L.262, D.268, I.270 Ligands: PO4.4 14 PLIP interactions: 12 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.202, B:L.261, B:L.262, B:I.270, B:I.270 Hydrogen bonds: B:G.132, B:Q.206, B:Q.206, B:R.208, B:R.208, A:H.25 Water bridges: B:R.127 pi-Stacking: B:F.202, A:Y.24

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 8 residues within 4Å: Chain A: G.48, G.49, R.127, I.128, G.129, T.130 Chain B: R.83 Ligands: BAU.1 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.49, A:T.130, A:E.239 Water bridges: A:R.127, A:M.238 Salt bridges: A:R.127, B:R.83 PO4.4: 10 residues within 4Å: Chain A: R.83 Chain B: G.48, G.49, R.53, R.127, I.128, G.129, T.130, E.239 Ligands: BAU.3 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.49, B:R.53, B:T.130, B:E.239 Water bridges: B:R.127 Salt bridges: B:R.127, A:R.83

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Roosild, T.P. et al., A novel structural mechanism for redox regulation of uridine phosphorylase 2 activity. J.Struct.Biol. (2011)

Release Date

2011-09-07

Peptides

Uridine phosphorylase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Uridine phosphorylase 2

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