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

Crystal Structure of Mouse Cytidine Deaminase Complexed with Cytidine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

homo-octamer

Ligands

8 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 ZN.11: 4 residues within 4Å: Chain E: C.65, C.99, C.102 Chain G: C.59 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:C.65, E:C.99, E:C.102, H2O.14 ZN.14: 5 residues within 4Å: Chain F: C.65, C.99, C.102 Chain H: C.59 Ligands: URI.15 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:C.65, F:C.99, F:C.102 ZN.17: 5 residues within 4Å: Chain E: C.59 Chain G: C.65, R.68, C.99, C.102 4 PLIP interactions: 3 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:C.65, G:C.99, G:C.102, H2O.21 ZN.19: 5 residues within 4Å: Chain F: C.59 Chain H: C.65, R.68, C.99, C.102 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:C.65, H:C.99, H:C.102, H2O.25

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

SO4.2: 7 residues within 4Å: Chain A: Q.130, P.134, A.135 Chain E: Q.130, A.135, S.136 Ligands: SO4.12 7 PLIP interactions: 3 interactions with chain E, 4 interactions with chain A Hydrogen bonds: E:Q.130, E:A.135, E:S.136, A:Q.130, A:A.135 Water bridges: A:S.136, A:S.136 SO4.12: 7 residues within 4Å: Chain A: Q.130, A.135, S.136 Chain E: Q.130, P.134, A.135 Ligands: SO4.2 7 PLIP interactions: 4 interactions with chain E, 3 interactions with chain A Hydrogen bonds: E:Q.130, E:A.135, A:Q.130, A:A.135, A:S.136 Water bridges: E:S.136, E:S.136

6 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: 7 interactions with chain C, 2 interactions with chain A, 1 interactions with chain D 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 pi-Stacking: D:F.137 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: 7 interactions with chain D, 2 interactions with chain B, 1 interactions with chain C 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 pi-Stacking: C:F.137 CTN.13: 16 residues within 4Å: Chain E: S.34, F.36, V.38, N.54, E.56, V.64, C.65, A.66, E.67, I.96, S.97 Chain F: F.137 Chain G: A.58, C.59, Y.60, P.61 9 PLIP interactions: 6 interactions with chain E, 2 interactions with chain G, 1 interactions with chain F Hydrogen bonds: E:N.54, E:E.56, E:A.66, E:E.67, E:S.97, G:A.58, G:Y.60 Water bridges: E:C.99 pi-Stacking: F:F.137 CTN.18: 16 residues within 4Å: Chain E: A.58, C.59, Y.60, P.61 Chain G: S.34, F.36, V.38, N.54, E.56, V.64, C.65, A.66, E.67, I.96, S.97 Chain H: F.137 10 PLIP interactions: 2 interactions with chain E, 7 interactions with chain G, 1 interactions with chain H Hydrogen bonds: E:A.58, E:Y.60, G:N.54, G:E.56, G:E.56, G:A.66, G:E.67, G:S.97 Water bridges: G:C.99 pi-Stacking: H:F.137 CTN.20: 16 residues within 4Å: Chain F: A.58, C.59, Y.60, P.61 Chain G: F.137 Chain H: 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: 2 interactions with chain F, 7 interactions with chain H, 1 interactions with chain G Hydrogen bonds: F:A.58, F:Y.60, H:N.54, H:E.56, H:E.56, H:A.66, H:E.67, H:S.97 Water bridges: H:C.99 pi-Stacking: G:F.137

2 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: 4 interactions with chain B, 1 interactions with chain A, 2 interactions with chain D Hydrogen bonds: B:N.54, B:A.66, B:E.67, B:C.99, D:A.58, D:Y.60 Hydrophobic interactions: A:F.137 URI.15: 20 residues within 4Å: Chain E: F.137, L.142 Chain F: 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 H: A.58, C.59, Y.60, P.61 Ligands: ZN.14, NH3.16 7 PLIP interactions: 2 interactions with chain H, 4 interactions with chain F, 1 interactions with chain E Hydrogen bonds: H:A.58, H:Y.60, F:N.54, F:A.66, F:E.67, F:C.99 Hydrophobic interactions: E:F.137

2 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 NH3.16: 5 residues within 4Å: Chain F: E.67, I.96, S.97, P.98 Ligands: URI.15 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:S.97

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: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
A

F
B

G
C

H
D

Cytidine deaminase

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