SMTL ID : 6k63.1 (1 other biounit)

The crystal structure of cytidine deaminase from Klebsiella pneumoniae

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

homo-dimer

Ligands

6 x DIO: 1,4-DIETHYLENE DIOXIDE(Non-covalent)

DIO.1: 4 residues within 4Å: Chain A: H.182, A.204, H.208, P.210 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.208 DIO.2: 5 residues within 4Å: Chain A: Y.126, T.127, C.129 Chain B: F.165 Ligands: DIO.4 1 PLIP interactions: 1 interactions with chain A Water bridges: A:C.129 DIO.4: 6 residues within 4Å: Chain A: F.71 Chain B: F.165, L.170, A.231, F.233 Ligands: DIO.2 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.89, A:N.89 DIO.5: 4 residues within 4Å: Chain B: H.182, A.204, H.208, P.210 No protein-ligand interaction detected (PLIP) DIO.6: 4 residues within 4Å: Chain A: F.165 Chain B: V.73, Y.126, T.127 1 PLIP interactions: 1 interactions with chain B Water bridges: B:C.129 DIO.7: 6 residues within 4Å: Chain A: F.165, L.170, A.231, F.233 Chain B: S.69, F.71 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.69 Water bridges: B:N.89, B:N.89

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 3 residues within 4Å: Chain A: H.102, C.129, C.132 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.102, A:C.129, A:C.132, H2O.9 ZN.8: 3 residues within 4Å: Chain B: H.102, C.129, C.132 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.102, B:C.129, B:C.132, H2O.20

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, W. et al., Biochemical and structural analysis of the Klebsiella pneumoniae cytidine deaminase CDA. Biochem.Biophys.Res.Commun. (2019)

Release Date

2019-07-31

Peptides

Cytidine deaminase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cytidine deaminase

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