MolNFT v1 · #59626 · protein
Evolution of chlorella virus dutpase
3C3I · Deoxyuridine triphosphatase: “Evolution of chlorella virus dutpase”. X-ray diffraction, 2 ligands (DUD, MG), 4 pockets (best druggability 0.78). MolNFT v1 #59626 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3C3I
- Type
- protein
- Length
- 529 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxyuridine triphosphatase
- EC
- 3.6.1.23
- UniProt
- Q5I3E5
- Ligands
- DUD, MG
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxyuridine triphosphatase (EC 3.6.1.23) | protein | 127 | 6% helix, 44% strand | Q5I3E5 |
| B, C | Deoxyuridine triphosphatase (EC 3.6.1.23) | protein | 136 | 5% helix, 40% strand | Q5I3E5 |
| D | Deoxyuridine triphosphatase (EC 3.6.1.23) | protein | 130 | 4% helix, 45% strand | Q5I3E5 |
Ligands and binding sites
- DUD · Deoxyuridine-5'-diphosphate · ligand · 4 copies · chains A, C, B, D
- MG · Magnesium ion · metal · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 121 | 0.78 | 0.97 | 30 | MG |
| 2 | 186 | 0.63 | 0.84 | 33 | DUD |
| 3 | 169 | 0.56 | 0.81 | 33 | DUD |
| 4 | 180 | 0.52 | 0.78 | 28 | DUD |
Interfaces
4 interfaces between chains.
- B–C · 1952 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 1817 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 1754 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 236 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3C3I · Evolution of chlorella virus dUTPase · 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 Q5I3E5
- Elsewhere: RCSB PDB 3C3I · PDBe 3C3I · UniProt Q5I3E5
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