MolNFT v1 · #29494 · protein
Crystal structure of mouse cytidine deaminase complexed with 3-deazauridine
1ZAB: “Crystal structure of mouse cytidine deaminase complexed with 3-deazauridine”. X-ray diffraction, 3 ligands (URD, ZN, SO4), 6 pockets (best druggability 0.81). MolNFT v1 #29494 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1ZAB
- Type
- protein
- Length
- 544 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytidine deaminase
- EC
- 3.5.4.5
- UniProt
- P56389
- Ligands
- URD, ZN, SO4
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Cytidine deaminase (EC 3.5.4.5) | protein | 137 | 34% helix, 23% strand | P56389 |
| B | Cytidine deaminase (EC 3.5.4.5) | protein | 134 | 36% helix, 25% strand | P56389 |
| C | Cytidine deaminase (EC 3.5.4.5) | protein | 136 | 36% helix, 24% strand | P56389 |
Ligands and binding sites
- URD · 1-((2R,3R,4S,5R)-tetrahydro-3,4-dihydroxy-5-(hydroxymethyl)furan-2-yl)pyridine-2,4(1H,3H)-dione · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, C, B, D
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 190 | 0.81 | 0.95 | 30 | empty |
| 2 | 90 | 0.78 | 0.99 | 22 | URD |
| 3 | 90 | 0.78 | 0.98 | 26 | URD |
| 4 | 85 | 0.76 | 0.98 | 23 | ZN, URD |
| 5 | 90 | 0.76 | 0.97 | 22 | URD |
Interfaces
6 interfaces between chains.
- A–D · 1356 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1281 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 906 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 860 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 475 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1ZAB · Crystal Structure of Mouse Cytidine Deaminase Complexed with 3-Deazauridine · the same entry in another collection · chain D against D, TM-score 1.00
- P56389 · AlphaFold monomer V2.0 prediction for cytidine deaminase (P56389) · a predicted model of the same protein · chain B against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P56389
- Elsewhere: RCSB PDB 1ZAB · PDBe 1ZAB · UniProt P56389
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