SMTL ID : 8vlj.1

Crystal structure of the cacodylate-bound yeast cytosine deaminase (closed form)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.39 Å

Oligo State

homo-dimer

Ligands

2 x CAC: CACODYLATE ION(Non-covalent)

CAC.1: 13 residues within 4Å: Chain A: I.36, H.65, G.66, E.67, L.91, S.92, P.93, C.94, C.97, W.155, D.158, I.159 Ligands: ZN.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.66, A:C.94 CAC.5: 13 residues within 4Å: Chain B: I.36, H.65, G.66, E.67, L.91, S.92, P.93, C.94, C.97, W.155, D.158, I.159 Ligands: ZN.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.66, B:C.94

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

EDO.2: 3 residues within 4Å: Chain A: R.151, Q.153, D.154 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Water bridges: B:R.76 Hydrogen bonds: A:R.151, A:R.151, A:Q.153 EDO.3: 3 residues within 4Å: Chain A: Y.29, E.150, R.151 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.151 Water bridges: A:G.32

2 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: H.65, C.94, C.97 Ligands: CAC.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.65, A:C.94, A:C.97 ZN.6: 4 residues within 4Å: Chain B: H.65, C.94, C.97 Ligands: CAC.5 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.65, B:C.94, B:C.97

1 x NA: SODIUM ION(Non-functional Binders)

NA.7: 1 residues within 4Å: Chain B: K.118 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.118, B:K.118

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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