MolNFT v1 · #120059 · protein
Crystal structure of uracil DNA glycosylase-uracil complex from bradyrhizobium diazoefficiens.
5GNW · BLR0248 protein: “Crystal structure of uracil DNA glycosylase-uracil complex from bradyrhizobium diazoefficiens.”. X-ray diffraction, 1 ligand (URA), 20 pockets (best druggability 0.78). MolNFT v1 #120059 on GenesisL1: 3D structure…
- PDB
- 5GNW
- Type
- protein
- Length
- 2,176 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BLR0248 protein
- UniProt
- Q89XR0
- Ligands
- URA
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D, E, F, A, B, G, H | BLR0248 protein | protein | 272 | 34% helix, 11% strand | Q89XR0 |
Ligands and binding sites
- URA · Uracil · ligand · 8 copies · chains C, D, E, F, A, B, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 109 | 0.78 | 0.97 | 34 | empty |
| 2 | 112 | 0.78 | 0.97 | 34 | empty |
| 3 | 95 | 0.77 | 0.97 | 24 | empty |
| 4 | 97 | 0.76 | 0.97 | 24 | empty |
| 5 | 587 | 0.75 | 0.82 | 62 | empty |
Interfaces
11 interfaces between chains.
- G–H · 1830 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1775 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 1759 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1725 Ų buried · 21 hydrogen bonds · protein-protein
- F–A · 467 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 modified (engineered).
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 Q89XR0
- Elsewhere: RCSB PDB 5GNW · PDBe 5GNW · UniProt Q89XR0
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