SMTL ID : 4eg2.3 (3 other biounits)

2.2 Angstrom Crystal Structure of Cytidine deaminase from Vibrio cholerae in Complex with Zinc and Uridine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.105, C.132, C.135 Ligands: URI.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.105, A:C.132, A:C.135 ZN.6: 4 residues within 4Å: Chain B: H.105, C.132, C.135 Ligands: URI.7 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.105, B:C.132, B:C.135

2 x URI: URIDINE(Non-covalent)

URI.2: 18 residues within 4Å: Chain A: F.74, V.76, N.92, E.94, T.103, V.104, H.105, A.106, E.107, S.130, P.131, C.132, C.135 Chain B: F.168, A.235, A.236, F.237 Ligands: ZN.1 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.92, A:H.105, A:A.106, A:E.107, A:C.132, B:A.235 pi-Cation interactions: A:H.105 pi-Stacking: B:F.168 URI.7: 17 residues within 4Å: Chain A: A.235, A.236, F.237 Chain B: F.74, V.76, N.92, E.94, T.103, V.104, H.105, A.106, E.107, F.129, P.131, C.132, C.135 Ligands: ZN.6 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.92, B:H.105, B:A.106, B:E.107, B:C.132, A:A.235 pi-Cation interactions: B:H.105 pi-Stacking: A:F.168

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 3 residues within 4Å: Chain A: Y.68, E.256, F.258 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.258 Hydrogen bonds: A:F.258 ACT.4: 6 residues within 4Å: Chain A: S.67, Y.68, A.69, P.70, E.73, Y.75 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.69 Salt bridges: A:R.7 ACT.5: 4 residues within 4Å: Chain A: D.54, V.57, K.154, R.155 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.57 Hydrogen bonds: A:D.54, A:Q.151, A:K.154, A:R.155 ACT.8: 4 residues within 4Å: Chain B: Y.68, E.256, S.257, F.258 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.68, B:F.258 Hydrogen bonds: B:F.258 Water bridges: B:E.259

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Minasov, G. et al., 2.2 Angstrom Crystal Structure of Cytidine deaminase from Vibrio cholerae in Complex with Zinc and Uridine. TO BE PUBLISHED

Release Date

2012-05-02

Peptides

Cytidine deaminase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

Cytidine deaminase

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