MolNFT v1 · #123848 · protein
New improved structure of D4 in trigonal space group
5JX8 · Uracil-DNA glycosylase: “New improved structure of D4 in trigonal space group”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.57). MolNFT v1 #123848 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5JX8
- Type
- protein
- Length
- 448 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uracil-DNA glycosylase
- EC
- 3.2.2.27
- UniProt
- P04303
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uracil-DNA glycosylase (EC 3.2.2.27) | protein | 227 | 37% helix, 17% strand | P04303 |
| B | Uracil-DNA glycosylase (EC 3.2.2.27) | protein | 221 | 38% helix, 19% strand | P04303 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 101 | 0.57 | 0.85 | 26 | GOL |
| 2 | 83 | 0.53 | 0.85 | 17 | GOL |
| 3 | 178 | 0.52 | 0.78 | 23 | empty |
| 4 | 110 | 0.40 | 0.76 | 27 | SO4 |
| 5 | 82 | 0.38 | 0.77 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 650 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5JX8 · New improved structure of D4 in trigonal space group · 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 P04303
- Elsewhere: RCSB PDB 5JX8 · PDBe 5JX8 · UniProt P04303
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