SMTL ID : 8vlk.1 (1 other biounit)

Crystal structure of the yeast cytosine deaminase containing both open and closed active sites

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

homo-dimer

Ligands

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 2 residues within 4Å: Chain A: R.128 Chain B: K.120 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.128, A:R.128, B:K.120, B:K.120 EDO.2: 10 residues within 4Å: Chain A: I.36, N.54, H.65, S.92, C.94, F.117, W.155, D.158, I.159 Ligands: ZN.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.54, A:S.92, A:C.94, A:D.158 EDO.5: 3 residues within 4Å: Chain B: G.50, R.51, N.73 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.51, B:N.73 Water bridges: B:N.73 EDO.6: 9 residues within 4Å: Chain B: I.36, H.65, E.67, L.91, S.92, P.93, C.94, C.97 Ligands: ZN.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.91, B:C.94 Water bridges: B:G.66

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: H.65, C.94, C.97 Ligands: EDO.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.65, A:C.94, A:C.97, H2O.1 ZN.7: 5 residues within 4Å: Chain B: H.65, E.67, C.94, C.97 Ligands: EDO.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.65, B:C.94, B:C.97

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

SO4.4: 2 residues within 4Å: Chain A: K.120 Chain B: R.128 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Water bridges: B:R.128 Salt bridges: B:R.128, A:K.120

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Despres, P.C. et al., Compensatory mutations potentiate constructive neutral evolution by gene duplication. Science (2024)

Release Date

2024-08-21

Peptides

Cytosine deaminase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cytosine deaminase

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