MolNFT v1 · #102532 · protein
Arabidopsis thaliana dutpase with with magnesium and ALPHA,BETA-imido- dutp
4OOP · Deoxyuridine 5'-triphosphate nucleotidohydrolase: “Arabidopsis thaliana dutpase with with magnesium and ALPHA,BETA-imido- dutp”. X-ray diffraction, 2 ligands (DUP, MG), 4 pockets (best druggability 0.79). MolNFT v1 #102532 on…
- PDB
- 4OOP
- Type
- protein
- Length
- 402 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxyuridine 5'-triphosphate nucleotidohydrolase
- EC
- 3.6.1.23
- UniProt
- Q9STG6
- Ligands
- DUP, MG
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 133 | 5% helix, 43% strand | Q9STG6 |
| B | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 142 | 5% helix, 42% strand | Q9STG6 |
| C | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 127 | 6% helix, 45% strand | Q9STG6 |
Ligands and binding sites
- DUP · 2'-deoxyuridine 5'-alpha,beta-imido-triphosphate · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 126 | 0.79 | 0.98 | 26 | empty |
| 2 | 132 | 0.77 | 0.95 | 32 | MG, DUP |
| 3 | 175 | 0.50 | 0.78 | 26 | DUP, MG |
| 4 | 148 | 0.45 | 0.76 | 27 | DUP, MG |
Interfaces
3 interfaces between chains.
- A–B · 2137 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 1899 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 1685 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 4OOP · Arabidopsis thaliana dUTPase with with magnesium and alpha,beta-imido-dUTP · the same entry in another collection · chain A against A, TM-score 1.00
- Q9STG6 · AlphaFold monomer V2.0 prediction for deoxyuridine 5'-triphosphate nucleotidohydrolase… · a predicted model of the same protein · chain B against A, TM-score 0.97
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 Q9STG6
- Elsewhere: RCSB PDB 4OOP · PDBe 4OOP · UniProt Q9STG6
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