SMTL ID : 1jtk.1

Crystal structure of cytidine deaminase from Bacillus subtilis in complex with the inhibitor tetrahydrodeoxyuridine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.04 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.86, C.89 Ligands: THU.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.53, A:C.86, A:C.89 ZN.3: 5 residues within 4Å: Chain B: C.53, E.55, C.86, C.89 Ligands: THU.4 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.53, B:C.86, B:C.89 ZN.5: 5 residues within 4Å: Chain C: C.53, E.55, C.86, C.89 Ligands: THU.6 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.53, C:C.86, C:C.89 ZN.7: 5 residues within 4Å: Chain D: C.53, E.55, C.86, C.89 Ligands: THU.8 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.53, D:C.86, D:C.89

4 x THU: TETRAHYDRODEOXYURIDINE(Non-covalent)

THU.2: 16 residues within 4Å: Chain A: F.24, V.26, N.42, E.44, C.53, A.54, E.55, S.84, P.85, C.86, C.89 Chain B: F.125 Chain D: A.46, A.47, Y.48 Ligands: ZN.1 8 PLIP interactions: 5 interactions with chain A, 2 interactions with chain D, 1 interactions with chain B Hydrogen bonds: A:N.42, A:E.44, A:A.54, A:E.55, A:C.86, D:A.46, D:Y.48 Hydrophobic interactions: B:F.125 THU.4: 16 residues within 4Å: Chain A: F.125 Chain B: F.24, V.26, N.42, E.44, C.53, A.54, E.55, S.84, P.85, C.86, C.89 Chain C: A.46, A.47, Y.48 Ligands: ZN.3 8 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A, 2 interactions with chain C Hydrogen bonds: B:N.42, B:E.44, B:A.54, B:E.55, B:C.86, C:A.46, C:Y.48 Hydrophobic interactions: A:F.125 THU.6: 16 residues within 4Å: Chain B: A.46, A.47, Y.48 Chain C: F.24, V.26, N.42, E.44, C.53, A.54, E.55, S.84, P.85, C.86, C.89 Chain D: F.125 Ligands: ZN.5 7 PLIP interactions: 4 interactions with chain C, 2 interactions with chain B, 1 interactions with chain D Hydrogen bonds: C:N.42, C:A.54, C:E.55, C:C.86, B:A.46, B:Y.48 Hydrophobic interactions: D:F.125 THU.8: 16 residues within 4Å: Chain A: A.46, A.47, Y.48 Chain C: F.125 Chain D: F.24, V.26, N.42, E.44, C.53, A.54, E.55, S.84, P.85, C.86, C.89 Ligands: ZN.7 7 PLIP interactions: 4 interactions with chain D, 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: D:N.42, D:A.54, D:E.55, D:C.86, A:A.46, A:Y.48 Hydrophobic interactions: C:F.125

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Johansson, E. et al., Crystal structure of the tetrameric cytidine deaminase from Bacillus subtilis at 2.0 A resolution. Biochemistry (2002)

Release Date

2002-04-10

Peptides

cytidine deaminase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

cytidine deaminase