SMTL ID : 3p0f.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.54 Å

Oligo State

homo-dimer

Ligands

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

BAU.1: 15 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 14 PLIP interactions: 3 interactions with chain B, 11 interactions with chain A Hydrogen bonds: B:H.25, A:T.130, A:G.132, A:Q.206, A:Q.206, A:R.208, A:R.208 Water bridges: B:Y.24, A:T.130 pi-Stacking: B:Y.24, A:F.202 Hydrophobic interactions: A:F.202, A:I.270, A:I.270 BAU.5: 15 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.262, D.268, I.270 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.202, 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:T.130, B:T.130 pi-Stacking: B:F.202, A:Y.24

4 x CO: COBALT (II) ION(Non-covalent)

CO.2: 2 residues within 4Å: Chain A: H.195, A.231 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.195, A:A.231, H2O.4, H2O.7 CO.3: 2 residues within 4Å: Chain A: D.16, H.116 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.16, A:H.116, H2O.4, H2O.6, H2O.8, H2O.9 CO.6: 2 residues within 4Å: Chain B: H.195, A.231 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.195, B:A.231, H2O.16, H2O.19 CO.7: 2 residues within 4Å: Chain B: D.16, H.116 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.16, B:H.116, H2O.15, H2O.17, H2O.19, H2O.21

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 2 residues within 4Å: Chain A: D.263, D.266 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.263, A:D.266, H2O.9, H2O.12, H2O.12 MG.8: 2 residues within 4Å: Chain B: D.263, D.266 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.263, B:D.266, H2O.21, H2O.23, H2O.24

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
A

B
A

Uridine phosphorylase 2

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