SMTL ID : 3dmo.1

1.6 A crystal structure of cytidine deaminase from Burkholderia pseudomallei

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: C.61, C.96, C.99 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.61, A:C.96, A:C.99, H2O.2 ZN.3: 4 residues within 4Å: Chain B: C.61, E.63, C.96, C.99 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.61, B:C.96, B:C.99, H2O.5 ZN.6: 4 residues within 4Å: Chain C: C.61, E.63, C.96, C.99 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:C.61, C:C.96, C:C.99, H2O.7 ZN.8: 3 residues within 4Å: Chain D: C.61, C.96, C.99 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:C.61, D:C.96, D:C.99, H2O.12

4 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.2: 8 residues within 4Å: Chain A: S.30, N.50, E.52, C.59 Chain C: A.54, S.55, Y.56 Chain D: L.137 5 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: A:N.50, C:Y.56, D:L.137 Hydrogen bonds: A:N.50, C:Y.56 MRD.5: 7 residues within 4Å: Chain B: S.30, N.50, E.52, C.59 Chain D: A.54, S.55, Y.56 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:N.50, D:Y.56 Hydrogen bonds: B:N.50, B:E.52, D:Y.56 MRD.7: 7 residues within 4Å: Chain A: A.54, S.55, Y.56 Chain C: S.30, N.50, E.52, C.59 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:Y.56, C:N.50 Hydrogen bonds: A:Y.56, C:N.50, C:E.52 MRD.9: 9 residues within 4Å: Chain A: L.137 Chain B: A.54, S.55, Y.56 Chain D: S.30, F.32, N.50, E.52, C.59 8 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: D:F.32, A:L.137, B:Y.56, B:Y.56 Hydrogen bonds: D:N.50, D:E.52, B:A.54, B:Y.56

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

PO4.4: 2 residues within 4Å: Chain B: T.10, H.11 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.11 Water bridges: B:H.12 Salt bridges: B:H.11

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Seattle Structural Genomics Center for Infectious Disease (SSGCID), 1.6 A crystal structure of cytidine deaminase from Burkholderia pseudomallei. To be Published

Release Date

2008-07-15

Peptides

Cytidine deaminase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Cytidine deaminase