SMTL ID : 8vll.1

Crystal structure of the yeast cytosine deaminase (yCD) M100W mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.67 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: PO4.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.65, A:C.94, A:C.97 ZN.7: 3 residues within 4Å: Chain B: H.65, C.94, C.97 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.65, B:C.94, B:C.97, H2O.5

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 10 residues within 4Å: Chain A: I.36, H.65, G.66, E.67, L.91, S.92, P.93, C.94, C.97 Ligands: ZN.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.66, A:C.94 Water bridges: A:N.54 Salt bridges: A:H.65

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

EDO.3: 6 residues within 4Å: Chain A: F.117, K.118, S.119, K.120 Chain B: W.103 Ligands: EDO.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.120 EDO.4: 4 residues within 4Å: Chain A: P.107, R.128, G.129, H.130 No protein-ligand interaction detected (PLIP) EDO.5: 4 residues within 4Å: Chain A: K.118, S.119, K.120 Ligands: EDO.3 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.118, A:K.118 EDO.6: 3 residues within 4Å: Chain A: W.103 Chain B: D.158, I.159 No protein-ligand interaction detected (PLIP) EDO.8: 3 residues within 4Å: Chain B: E.31, H.53, M.55 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.53 EDO.9: 3 residues within 4Å: Chain B: N.54, H.65, D.158 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.54, B:D.158 Water bridges: B:C.94 EDO.10: 4 residues within 4Å: Chain B: P.107, R.128, G.129, H.130 No protein-ligand interaction detected (PLIP) EDO.11: 4 residues within 4Å: Chain B: R.151, P.152, Q.153, D.154 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.153, B:D.154, B:D.154

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