SMTL ID : 8x6u.1

Crystal structure of EfCDA in complex with dFdU

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.57, C.90, C.93 Ligands: Y7U.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.57, A:C.90, A:C.93 ZN.3: 4 residues within 4Å: Chain B: C.57, C.90, C.93 Ligands: Y7U.4 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.57, B:C.90, B:C.93 ZN.5: 4 residues within 4Å: Chain C: C.57, C.90, C.93 Ligands: Y7U.6 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.57, C:C.90, C:C.93 ZN.7: 4 residues within 4Å: Chain D: C.57, C.90, C.93 Ligands: Y7U.8 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.57, D:C.90, D:C.93

4 x Y7U: 2',2'-Difluorodeoxyuridine(Non-covalent)

Y7U.2: 18 residues within 4Å: Chain A: V.23, S.26, F.28, V.30, N.46, E.48, T.55, N.56, C.57, A.58, E.59, P.89, C.90, C.93 Chain D: A.50, S.51, F.52 Ligands: ZN.1 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:S.26, A:N.46, A:E.48, A:A.58, A:E.59, A:C.90, D:A.50, D:F.52 Halogen bonds: D:S.51 Y7U.4: 18 residues within 4Å: Chain B: F.28, V.30, N.46, E.48, T.55, N.56, C.57, A.58, E.59, P.89, C.90, C.93 Chain C: A.50, S.51, F.52 Chain D: F.129, L.134 Ligands: ZN.3 9 PLIP interactions: 3 interactions with chain C, 6 interactions with chain B Hydrogen bonds: C:A.50, C:F.52, B:S.26, B:N.46, B:A.58, B:E.59, B:C.90 Halogen bonds: C:S.51, B:N.56 Y7U.6: 18 residues within 4Å: Chain B: A.50, S.51, F.52 Chain C: V.23, S.26, F.28, V.30, N.46, E.48, T.55, N.56, C.57, A.58, E.59, P.89, C.90, C.93 Ligands: ZN.5 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:S.26, C:N.46, C:A.58, C:E.59, C:C.90, B:A.50, B:F.52 Halogen bonds: B:S.51 Y7U.8: 18 residues within 4Å: Chain A: A.50, S.51, F.52 Chain B: F.129, L.134 Chain D: F.28, V.30, N.46, E.48, T.55, N.56, C.57, A.58, E.59, P.89, C.90, C.93 Ligands: ZN.7 10 PLIP interactions: 7 interactions with chain D, 3 interactions with chain A Hydrogen bonds: D:S.26, D:N.46, D:E.48, D:A.58, D:E.59, D:C.90, A:A.50, A:F.52 Halogen bonds: D:N.56, A:S.51

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jiang, L. et al., Deciphering the role of Enterococcus faecium cytidine deaminase in gemcitabine resistance of gallbladder cancer. J.Biol.Chem. (2024)

Release Date

2024-11-27

Peptides

EfCDA: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

EfCDA

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