SMTL ID : 2fr6.1 (2 other biounits)

Crystal Structure of Mouse Cytidine Deaminase Complexed with Cytidine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.65, C.99, C.102 Chain C: C.59 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.65, A:C.99, A:C.102, H2O.1 ZN.4: 5 residues within 4Å: Chain B: C.65, C.99, C.102 Chain D: C.59 Ligands: URI.5 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.65, B:C.99, B:C.102 ZN.7: 5 residues within 4Å: Chain A: C.59 Chain C: C.65, R.68, C.99, C.102 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:C.65, C:C.99, C:C.102, H2O.8 ZN.9: 5 residues within 4Å: Chain B: C.59 Chain D: C.65, R.68, C.99, C.102 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:C.65, D:C.99, D:C.102, H2O.11

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 3 residues within 4Å: Chain A: Q.130, P.134, A.135 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.130, A:A.135 Water bridges: A:S.136, A:S.136

3 x CTN: 4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE(Non-covalent)

CTN.3: 16 residues within 4Å: Chain A: S.34, F.36, V.38, N.54, E.56, V.64, C.65, A.66, E.67, I.96, S.97 Chain B: F.137 Chain C: A.58, C.59, Y.60, P.61 9 PLIP interactions: 6 interactions with chain A, 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: A:N.54, A:E.56, A:A.66, A:E.67, A:S.97, C:A.58, C:Y.60 Water bridges: A:C.99 pi-Stacking: B:F.137 CTN.8: 16 residues within 4Å: Chain A: A.58, C.59, Y.60, P.61 Chain C: S.34, F.36, V.38, N.54, E.56, V.64, C.65, A.66, E.67, I.96, S.97 Chain D: F.137 10 PLIP interactions: 1 interactions with chain D, 7 interactions with chain C, 2 interactions with chain A pi-Stacking: D:F.137 Hydrogen bonds: C:N.54, C:E.56, C:E.56, C:A.66, C:E.67, C:S.97, A:A.58, A:Y.60 Water bridges: C:C.99 CTN.10: 16 residues within 4Å: Chain B: A.58, C.59, Y.60, P.61 Chain C: F.137 Chain D: S.34, F.36, V.38, N.54, E.56, V.64, C.65, A.66, E.67, I.96, S.97 10 PLIP interactions: 1 interactions with chain C, 7 interactions with chain D, 2 interactions with chain B pi-Stacking: C:F.137 Hydrogen bonds: D:N.54, D:E.56, D:E.56, D:A.66, D:E.67, D:S.97, B:A.58, B:Y.60 Water bridges: D:C.99

1 x URI: URIDINE(Non-covalent)

URI.5: 20 residues within 4Å: Chain A: F.137, L.142 Chain B: S.34, F.36, V.38, N.54, E.56, V.64, C.65, A.66, E.67, P.98, C.99, C.102 Chain D: A.58, C.59, Y.60, P.61 Ligands: ZN.4, NH3.6 7 PLIP interactions: 2 interactions with chain D, 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: D:A.58, D:Y.60, B:N.54, B:A.66, B:E.67, B:C.99 Hydrophobic interactions: A:F.137

1 x NH3: AMMONIA(Non-covalent)

NH3.6: 5 residues within 4Å: Chain B: E.67, I.96, S.97, P.98 Ligands: URI.5 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.67

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Teh, A.H. et al., The 1.48 A Resolution Crystal Structure of the Homotetrameric Cytidine Deaminase from Mouse. Biochemistry (2006)

Release Date

2006-07-11

Peptides

Cytidine deaminase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Cytidine deaminase

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