SMTL ID : 3kvr.1

Trapping of an oxocarbenium ion intermediate in UP crystals

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

2 x URF: 5-FLUOROURACIL(Non-covalent)

URF.1: 13 residues within 4Å: Chain A: T.140, S.141, G.142, F.212, Q.216, R.218, I.246, E.247, M.248, L.271, L.272, I.280 Ligands: R2G.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.140, A:G.142, A:Q.216, A:Q.216, A:R.218, A:R.218 URF.4: 13 residues within 4Å: Chain B: T.140, S.141, G.142, F.212, Q.216, R.218, I.246, E.247, M.248, L.271, L.272, I.280 Ligands: R2G.6 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.140, B:Q.216, B:Q.216, B:R.218, B:R.218

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

SO4.2: 11 residues within 4Å: Chain A: G.58, G.59, R.63, H.107, R.137, I.138, G.139, T.140, E.249 Chain B: R.93 Ligands: R2G.3 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.59, A:T.140, A:T.140 Salt bridges: A:R.63, A:R.137, B:R.93 Water bridges: B:R.93 SO4.5: 9 residues within 4Å: Chain A: R.93 Chain B: G.58, G.59, R.63, R.137, I.138, G.139, T.140 Ligands: R2G.6 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.59, B:T.140 Salt bridges: B:R.63, B:R.137, A:R.93

2 x R2G: 2,5-anhydro-4-deoxy-D-erythro-pent-4-enitol(Non-covalent)

R2G.3: 10 residues within 4Å: Chain A: M.109, G.110, R.137, T.140, F.212, E.249 Chain B: H.35, R.93 Ligands: URF.1, SO4.2 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.110, A:E.249, B:H.35, B:R.93 Water bridges: A:T.140 R2G.6: 10 residues within 4Å: Chain A: Y.34, H.35 Chain B: M.109, G.110, R.137, T.140, F.212, E.249 Ligands: URF.4, SO4.5 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:G.110, B:T.140, B:E.249, 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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