SMTL ID : 1p6o.1

The crystal structure of yeast cytosine deaminase bound to 4(R)-hydroxyl-3,4-dihydropyrimidine at 1.14 angstroms.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.14 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.65, E.67, C.94, C.97 Ligands: HPY.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.65, A:C.94, A:C.97 ZN.4: 5 residues within 4Å: Chain B: H.65, E.67, C.94, C.97 Ligands: HPY.7 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.65, B:C.94, B:C.97

2 x HPY: 4-HYDROXY-3,4-DIHYDRO-1H-PYRIMIDIN-2-ONE(Non-covalent)

HPY.2: 12 residues within 4Å: Chain A: I.36, N.54, H.65, G.66, E.67, P.93, C.94, C.97, W.155, D.158, I.159 Ligands: ZN.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.54, A:G.66, A:C.94, A:D.158 pi-Stacking: A:H.65 HPY.7: 11 residues within 4Å: Chain B: I.36, N.54, H.65, G.66, E.67, P.93, C.94, C.97, D.158, I.159 Ligands: ZN.4 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.54, B:G.66, B:C.94, B:D.158 pi-Stacking: B:H.65

3 x ACY: ACETIC ACID(Non-functional Binders)

ACY.3: 1 residues within 4Å: Chain A: D.45 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.45 Salt bridges: A:K.16 ACY.8: 4 residues within 4Å: Chain B: G.105, P.107, G.129, H.130 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.130 ACY.9: 3 residues within 4Å: Chain B: N.43, D.84, P.107 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.84, B:D.84 Water bridges: B:N.43

2 x CA: CALCIUM ION(Non-covalent)

CA.5: 1 residues within 4Å: Chain B: E.131 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.131, H2O.8, H2O.9, H2O.14 CA.6: 2 residues within 4Å: Chain A: Q.153 Chain B: E.78 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.78, H2O.4, H2O.6, H2O.15, H2O.16

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ireton, G.C. et al., The 1.14 a crystal structure of yeast Cytosine deaminase. Evolution of nucleotide salvage enzymes and implications for genetic chemotherapy. Structure (2003)

Release Date

2003-08-19

Peptides

Cytosine deaminase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cytosine deaminase

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