SMTL ID : 8i3p.1

crystal structure of yeast cytosine deaminase mutant yCD-RQ-1/8SAH in complex with (R)-4-hydroxy-3,4-dihydropyrimidin-2(1H)-one

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-dimer

Ligands

2 x OS0: 4-oxidanyl-3,4-dihydro-1H-pyrimidin-2-one

OS0.1: 13 residues within 4Å: Chain A: I.34, N.52, H.63, G.64, E.65, P.91, C.92, C.95, F.115, W.153, D.156, I.157 Ligands: ZN.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.115 Hydrogen bonds: A:N.52, A:G.64, A:C.92 OS0.4: 13 residues within 4Å: Chain B: I.34, N.52, H.63, G.64, E.65, P.91, C.92, C.95, F.115, W.153, D.156, I.157 Ligands: ZN.5 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.115 Hydrogen bonds: B:N.52, B:G.64, B:C.92, B:D.156 pi-Stacking: B:H.63

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: H.63, E.65, C.92, C.95 Ligands: OS0.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.63, A:C.92, A:C.95 ZN.5: 5 residues within 4Å: Chain B: H.63, E.65, C.92, C.95 Ligands: OS0.4 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.63, B:C.92, B:C.95

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

EDO.3: 2 residues within 4Å: Chain A: R.126 Chain B: K.118 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.126, A:R.126 EDO.6: 2 residues within 4Å: Chain A: K.118 Chain B: R.126 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.126, B:R.126, A:K.118

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Qin, M.M. et al., crystal structure of yeast cytosine deaminase mutant yCD-RQ-1/8SAH in complex with (R)-4-hydroxy-3,4-dihydropyrimidin-2(1H)-one. To be published

Release Date

2024-01-24

Peptides

Cytosine deaminase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cytosine deaminase