SMTL ID : 1mq0.1

Crystal Structure of Human Cytidine Deaminase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.59, E.61, C.93, C.96 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.59, A:C.93, A:C.96 ZN.3: 5 residues within 4Å: Chain A: C.53 Chain B: C.59, E.61, C.93, C.96 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.59, B:C.93, B:C.96, H2O.1 ZN.5: 4 residues within 4Å: Chain C: C.59, E.61, C.93, C.96 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.59, C:C.93, C:C.96 ZN.7: 5 residues within 4Å: Chain C: C.53 Chain D: C.59, E.61, C.93, C.96 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:C.59, D:C.93, D:C.96, H2O.4

4 x BRD: 1-BETA-RIBOFURANOSYL-1,3-DIAZEPINONE(Non-covalent)

BRD.2: 15 residues within 4Å: Chain A: S.28, F.30, V.32, N.48, E.50, I.58, C.59, A.60, E.61, S.91 Chain B: A.52, C.53, Y.54, P.55 Chain C: F.131 9 PLIP interactions: 2 interactions with chain C, 5 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: C:F.131, C:F.131 Hydrogen bonds: A:S.28, A:N.48, A:E.50, A:A.60, A:E.61, B:A.52, B:Y.54 BRD.4: 15 residues within 4Å: Chain A: A.52, C.53, Y.54, P.55 Chain B: F.30, V.32, N.48, E.50, I.58, C.59, A.60, E.61, I.90, S.91 Chain D: F.131 12 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D, 8 interactions with chain B Hydrogen bonds: A:A.52, A:Y.54, B:N.48, B:E.50, B:E.50, B:A.60, B:E.61 Hydrophobic interactions: D:F.131, D:F.131, B:I.90 Water bridges: B:I.49, B:I.49 BRD.6: 15 residues within 4Å: Chain A: F.131 Chain C: S.28, F.30, V.32, N.48, E.50, I.58, C.59, A.60, E.61, S.91 Chain D: A.52, C.53, Y.54, P.55 9 PLIP interactions: 5 interactions with chain C, 2 interactions with chain D, 2 interactions with chain A Hydrogen bonds: C:S.28, C:N.48, C:E.50, C:A.60, C:E.61, D:A.52, D:Y.54 Hydrophobic interactions: A:F.131, A:F.131 BRD.8: 15 residues within 4Å: Chain B: F.131 Chain C: A.52, C.53, Y.54, P.55 Chain D: F.30, V.32, N.48, E.50, I.58, C.59, A.60, E.61, I.90, S.91 12 PLIP interactions: 2 interactions with chain B, 8 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: B:F.131, B:F.131, D:I.90 Hydrogen bonds: D:N.48, D:E.50, D:E.50, D:A.60, D:E.61, C:A.52, C:Y.54 Water bridges: D:I.49, D:I.49

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chung, S.J. et al., Structure of human cytidine deaminase bound to a potent inhibitor. J.Med.Chem. (2005)

Release Date

2003-11-04

Peptides

Cytidine Deaminase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Cytidine Deaminase