MolNFT v1 · #105589 · protein
Crystal structure of a uricase from bacillus fastidious
4R99: “Crystal structure of a uricase from bacillus fastidious”. X-ray diffraction, 1 ligand (SO4), 17 pockets (best druggability 0.80). MolNFT v1 #105589 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4R99
- Type
- protein
- Length
- 1,277 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uricase
- EC
- 3.1.2.4
- UniProt
- C5HDG5
- Ligands
- SO4
- Pockets
- 17 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 26% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uricase (EC 3.1.2.4) | protein | 317 | 26% helix, 38% strand | C5HDG5 |
| B | Uricase (EC 3.1.2.4) | protein | 317 | 26% helix, 38% strand | C5HDG5 |
| C | Uricase (EC 3.1.2.4) | protein | 321 | 26% helix, 39% strand | C5HDG5 |
| D | Uricase (EC 3.1.2.4) | protein | 322 | 26% helix, 39% strand | C5HDG5 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 879 | 0.80 | 0.82 | 92 | empty |
| 2 | 867 | 0.78 | 0.81 | 82 | empty |
| 3 | 430 | 0.73 | 0.83 | 37 | SO4 |
| 4 | 62 | 0.73 | 0.98 | 17 | empty |
| 5 | 677 | 0.72 | 0.79 | 81 | SO4 |
Interfaces
6 interfaces between chains.
- A–C · 2916 Ų buried · 53 hydrogen bonds · protein-protein
- B–D · 2819 Ų buried · 50 hydrogen bonds · protein-protein
- A–B · 2727 Ų buried · 43 hydrogen bonds · protein-protein
- C–D · 2722 Ų buried · 40 hydrogen bonds · protein-protein
- A–D · 262 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4R99 · Crystal structure of a uricase from Bacillus fastidious · 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 C5HDG5
- Elsewhere: RCSB PDB 4R99 · PDBe 4R99 · UniProt C5HDG5
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