MolNFT v1 · #55929 · protein
Crystal structure of dctp deaminase from sulfolobus tokodaii
2YZJ · 167AA long hypothetical dutpase: “Crystal structure of dctp deaminase from sulfolobus tokodaii”. X-ray diffraction, 2 ligands (DUD, MG), 5 pockets (best druggability 0.70). MolNFT v1 #55929 on GenesisL1: 3D structure, binding sites…
- PDB
- 2YZJ
- Type
- protein
- Length
- 474 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 167AA long hypothetical dutpase
- UniProt
- Q970G0
- Ligands
- DUD, MG
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 8% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | 167AA long hypothetical dutpase | protein | 158 | 8% helix, 50% strand | Q970G0 |
Ligands and binding sites
- DUD · Deoxyuridine-5'-diphosphate · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 265 | 0.70 | 0.85 | 40 | DUD |
| 2 | 245 | 0.70 | 0.85 | 40 | DUD |
| 3 | 265 | 0.69 | 0.84 | 42 | DUD |
| 4 | 57 | 0.65 | 0.94 | 18 | TRS |
| 5 | 161 | 0.60 | 0.83 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1679 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 1675 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 1670 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified, 3 disulfide (engineered, disulfide).
Compared structures
- 2YZJ · Crystal structure of dCTP deaminase from Sulfolobus tokodaii · the same entry in another collection · chain A against A, TM-score 1.00
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 Q970G0
- Elsewhere: RCSB PDB 2YZJ · PDBe 2YZJ · UniProt Q970G0
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