Research workbench
Crystal structure of uricase from Arthrobacter globiformis
Analyse Crystal structure of uricase from Arthrobacter globiformis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YZE
- Type
- protein
- Length
- 2,296 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.99
- Source
- Arthrobacter globiformis
- Molecule
- Uricase
- EC
- 1.7.3.3
- Ligands
- NOB
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · resolution 1.99 · 1 distinct chain · 25% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Uricase (EC 1.7.3.3) | protein | 287 | 25% helix, 42% strand | — |
Ligands and binding sites
- NOB · (dihydroxyboranyloxy-hydroxy-boranyl)oxylithium · ligand · 8 copies · chains A, D, B, C, E, H, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1004 | 0.80 | 0.81 | 100 | NOB |
| 2 | 971 | 0.79 | 0.81 | 98 | NOB |
| 3 | 892 | 0.77 | 0.79 | 83 | NOB |
| 4 | 852 | 0.76 | 0.79 | 83 | NOB |
| 5 | 986 | 0.71 | 0.76 | 94 | empty |
Interfaces
15 interfaces between chains.
- F–G · 3304 Ų buried · 56 hydrogen bonds · protein-protein
- B–C · 3302 Ų buried · 56 hydrogen bonds · protein-protein
- E–H · 3263 Ų buried · 55 hydrogen bonds · protein-protein
- A–D · 3262 Ų buried · 56 hydrogen bonds · protein-protein
- G–H · 2465 Ų buried · 51 hydrogen bonds · protein-protein
Compared structures
- 2YZE · Crystal structure of uricase from arthrobacter globiformis · 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
- Elsewhere: RCSB PDB 2YZE · PDBe 2YZE
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