SMTL ID : 3kvy.1

Trapping of an oxocarbenium ion intermediate in UP crystals

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: Y.126, H.127, H.129 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.126 Salt bridges: A:H.127, A:H.129 SO4.2: 8 residues within 4Å: Chain A: G.58, G.59, R.137, I.138, G.139, T.140 Chain B: R.93 Ligands: R2B.4 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.59, A:T.140 Salt bridges: A:R.137, B:R.93 SO4.5: 2 residues within 4Å: Chain B: Y.126, H.127 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.127 SO4.6: 8 residues within 4Å: Chain A: R.93 Chain B: G.58, G.59, R.137, I.138, G.139, T.140 Ligands: R2B.8 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.59, B:I.138, B:T.140 Salt bridges: B:R.137, A:R.93

2 x URA: URACIL(Non-covalent)

URA.3: 11 residues within 4Å: Chain A: T.140, S.141, G.142, F.212, Q.216, R.218, I.246, E.247, M.248, L.272 Ligands: R2B.4 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.212 Hydrogen bonds: A:T.140, A:G.142, A:Q.216, A:Q.216, A:R.218, A:R.218 Water bridges: A:T.140 URA.7: 12 residues within 4Å: Chain B: T.140, S.141, G.142, F.212, Q.216, R.218, I.246, E.247, M.248, L.272, R.274 Ligands: R2B.8 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.212 Hydrogen bonds: B:T.140, B:T.140, B:G.142, B:Q.216, B:Q.216, B:R.218, B:R.218

2 x R2B: 1,4-anhydro-D-erythro-pent-1-enitol(Non-covalent)

R2B.4: 10 residues within 4Å: Chain A: M.109, R.137, T.140, F.212, E.247, M.248, E.249 Chain B: H.35 Ligands: SO4.2, URA.3 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:T.140, A:M.248, B:H.35 Water bridges: B:R.93, B:R.93 R2B.8: 10 residues within 4Å: Chain A: H.35 Chain B: M.109, R.137, T.140, F.212, E.247, M.248, E.249 Ligands: SO4.6, URA.7 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:T.140, B:E.247, B:M.248, A:H.35 Water bridges: A:R.93, A:R.93

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Paul, D. et al., Glycal formation in crystals of uridine phosphorylase. Biochemistry (2010)

Release Date

2010-04-28

Peptides

Uridine Phosphorylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Uridine Phosphorylase

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