SMTL ID : 9hft.1

Cryo-EM structure of human CDADC1 inactive mutant (E400A): hexamer with 5mdCTP bound in the active site

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

12 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.129, C.154, C.157, E.177 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.129, A:C.154, A:C.157, A:E.177 ZN.2: 4 residues within 4Å: Chain A: H.418, C.446, C.449 Ligands: 01.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.418, A:C.446, A:C.449 ZN.4: 4 residues within 4Å: Chain B: H.129, C.154, C.157, E.177 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.129, B:C.154, B:C.157, B:E.177 ZN.5: 4 residues within 4Å: Chain B: H.418, C.446, C.449 Ligands: 01.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.418, B:C.446, B:C.449 ZN.7: 4 residues within 4Å: Chain C: H.129, C.154, C.157, E.177 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.129, C:C.154, C:C.157, C:E.177 ZN.8: 4 residues within 4Å: Chain C: H.418, C.446, C.449 Ligands: 01.9 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.418, C:C.446, C:C.449 ZN.10: 4 residues within 4Å: Chain D: H.129, C.154, C.157, E.177 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.129, D:C.154, D:C.157, D:E.177 ZN.11: 4 residues within 4Å: Chain D: H.418, C.446, C.449 Ligands: 01.12 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.418, D:C.446, D:C.449 ZN.13: 4 residues within 4Å: Chain E: H.129, C.154, C.157, E.177 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.129, E:C.154, E:C.157, E:E.177 ZN.14: 4 residues within 4Å: Chain E: H.418, C.446, C.449 Ligands: 01.15 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:H.418, E:C.446, E:C.449 ZN.16: 4 residues within 4Å: Chain F: H.129, C.154, C.157, E.177 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.129, F:C.154, F:C.157, F:E.177 ZN.17: 4 residues within 4Å: Chain F: H.418, C.446, C.449 Ligands: 01.18 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:H.418, F:C.446, F:C.449

6 x 01: [[(2~{R},3~{S},5~{R})-5-(4-azanyl-5-methyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate

01.3: 19 residues within 4Å: Chain A: D.355, K.357, T.358, V.360, N.387, K.412, F.413, I.416, H.418, A.419, C.444, P.445, C.446, C.449, K.470, K.472, I.475, Y.477 Ligands: ZN.2 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:I.416, A:I.475, A:Y.477 Hydrogen bonds: A:T.358, A:N.387, A:A.419, A:C.444, A:C.446 Water bridges: A:A.420 Salt bridges: A:K.357, A:K.357, A:K.357, A:K.412, A:K.470, A:K.470, A:K.472, A:K.472, A:K.472 pi-Stacking: A:H.418 01.6: 19 residues within 4Å: Chain B: D.355, K.357, T.358, V.360, N.387, K.412, F.413, I.416, H.418, A.419, C.444, P.445, C.446, C.449, K.470, K.472, I.475, Y.477 Ligands: ZN.5 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:I.416, B:I.475, B:Y.477 Hydrogen bonds: B:T.358, B:N.387, B:A.419, B:C.444, B:C.446, B:Y.477 Water bridges: B:A.420 Salt bridges: B:K.357, B:K.357, B:K.357, B:K.412, B:K.470, B:K.470, B:K.472, B:K.472, B:K.472 pi-Stacking: B:H.418 01.9: 19 residues within 4Å: Chain C: D.355, K.357, T.358, V.360, N.387, K.412, F.413, I.416, H.418, A.419, C.444, P.445, C.446, C.449, K.470, K.472, I.475, Y.477 Ligands: ZN.8 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:I.416, C:I.475, C:Y.477 Hydrogen bonds: C:T.358, C:N.387, C:A.419, C:C.444, C:C.446, C:Y.477 Water bridges: C:A.420 Salt bridges: C:K.357, C:K.357, C:K.357, C:K.412, C:K.470, C:K.470, C:K.472, C:K.472, C:K.472 pi-Stacking: C:H.418 01.12: 19 residues within 4Å: Chain D: D.355, K.357, T.358, V.360, N.387, K.412, F.413, I.416, H.418, A.419, C.444, P.445, C.446, C.449, K.470, K.472, I.475, Y.477 Ligands: ZN.11 20 PLIP interactions: 20 interactions with chain D Hydrophobic interactions: D:I.416, D:I.475, D:Y.477 Hydrogen bonds: D:N.387, D:A.419, D:C.444, D:C.446, D:Y.477, D:Y.477 Water bridges: D:A.420 Salt bridges: D:K.357, D:K.357, D:K.357, D:K.412, D:K.470, D:K.470, D:K.472, D:K.472, D:K.472 pi-Stacking: D:H.418 01.15: 18 residues within 4Å: Chain E: D.355, K.357, T.358, V.360, N.387, K.412, F.413, I.416, H.418, A.419, C.444, P.445, C.446, K.470, K.472, I.475, Y.477 Ligands: ZN.14 20 PLIP interactions: 20 interactions with chain E Hydrophobic interactions: E:I.416, E:I.475, E:Y.477 Hydrogen bonds: E:N.387, E:A.419, E:C.444, E:C.446, E:Y.477, E:Y.477 Water bridges: E:A.420 Salt bridges: E:K.357, E:K.357, E:K.357, E:K.412, E:K.470, E:K.470, E:K.472, E:K.472, E:K.472 pi-Stacking: E:H.418 01.18: 19 residues within 4Å: Chain F: D.355, K.357, T.358, V.360, N.387, K.412, F.413, I.416, H.418, A.419, C.444, P.445, C.446, C.449, K.470, K.472, I.475, Y.477 Ligands: ZN.17 18 PLIP interactions: 18 interactions with chain F Hydrophobic interactions: F:I.475, F:Y.477 Hydrogen bonds: F:T.358, F:N.387, F:A.419, F:C.444, F:C.446 Water bridges: F:A.420 Salt bridges: F:K.357, F:K.357, F:K.357, F:K.412, F:K.470, F:K.470, F:K.472, F:K.472, F:K.472 pi-Stacking: F:H.418

Links

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Citation

Slyvka, A. et al., Cryo-EM structure of human CDADC1 inactive mutant (E400A): trimer without a ligand. To Be Published (2025)

Release Date

2025-04-30

Peptides

Cytidine and dCMP deaminase domain-containing protein 1: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Cytidine and dCMP deaminase domain-containing protein 1

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