SMTL ID : 7zob.1 (2 other biounits)

Metagenomic cytidine deaminase Cdd

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.53, E.55, C.88, C.91 Ligands: MPD.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.53, A:C.88, A:C.91, H2O.1 ZN.4: 5 residues within 4Å: Chain B: C.53, E.55, C.88, C.91 Ligands: MPD.5 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.53, B:C.88, B:C.91, H2O.4 ZN.7: 3 residues within 4Å: Chain C: C.53, C.88, C.91 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:C.53, C:C.88, C:C.91, H2O.8 ZN.10: 5 residues within 4Å: Chain D: C.53, E.55, C.88, C.91 Ligands: MPD.12 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:C.53, D:C.88, D:C.91, H2O.11

8 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.2: 11 residues within 4Å: Chain A: S.22, Y.24, N.42, E.44, T.51, C.53 Chain B: F.126, L.131 Chain D: A.46, S.47, Y.48 10 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: B:F.126, B:L.131, A:Y.24, A:N.42, A:T.51, D:Y.48 Hydrogen bonds: A:N.42, A:E.44, D:A.46, D:Y.48 MPD.3: 8 residues within 4Å: Chain A: Y.24, I.77, T.79, G.85, A.86, C.88 Chain B: F.126 Ligands: ZN.1 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.24, A:I.77, A:T.79, B:F.126, B:F.126 Water bridges: A:A.86 MPD.5: 9 residues within 4Å: Chain A: F.126 Chain B: Y.24, V.26, I.77, T.79, G.85, A.86, C.88 Ligands: ZN.4 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:F.126, A:F.126, B:Y.24, B:V.26, B:I.77, B:T.79 MPD.6: 11 residues within 4Å: Chain A: F.126, L.131 Chain B: S.22, Y.24, N.42, E.44, T.51, C.53 Chain C: A.46, S.47, Y.48 10 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: A:F.126, A:L.131, C:Y.48, B:Y.24, B:N.42, B:T.51 Hydrogen bonds: C:A.46, C:Y.48, B:N.42, B:E.44 MPD.8: 11 residues within 4Å: Chain B: A.46, S.47, Y.48 Chain C: S.22, Y.24, N.42, E.44, T.51, C.53 Chain D: F.126, L.131 11 PLIP interactions: 3 interactions with chain B, 2 interactions with chain D, 6 interactions with chain C Hydrophobic interactions: B:Y.48, D:F.126, D:L.131, C:Y.24, C:N.42, C:T.51 Hydrogen bonds: B:A.46, B:Y.48, C:N.42, C:E.44, C:E.44 MPD.9: 8 residues within 4Å: Chain C: Y.24, V.26, I.77, T.79, G.85, A.86, C.88 Chain D: F.126 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:Y.24, C:V.26, C:I.77, C:T.79, D:F.126 MPD.11: 11 residues within 4Å: Chain A: A.46, S.47, Y.48 Chain C: F.126, L.131 Chain D: S.22, Y.24, N.42, E.44, T.51, C.53 11 PLIP interactions: 6 interactions with chain D, 2 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: D:Y.24, D:N.42, D:T.51, C:F.126, C:L.131, A:Y.48 Hydrogen bonds: D:N.42, D:E.44, D:E.44, A:A.46, A:Y.48 MPD.12: 9 residues within 4Å: Chain C: F.126 Chain D: Y.24, V.26, I.77, T.79, G.85, A.86, C.88 Ligands: ZN.10 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:Y.24, D:V.26, D:I.77, D:T.79, C:F.126, C:F.126

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Urbeliene, N. et al., Cytidine deaminases catalyze the conversion of N ( S , O ) 4 -substituted pyrimidine nucleosides. Sci Adv (2023)

Release Date

2023-02-01

Peptides

Metagenomic cytidine deaminase Cdd: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Metagenomic cytidine deaminase Cdd

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