Research workbench
Crystal structure of uricase from arthrobacter globiformis in complex with allantoate
Analyse Crystal structure of uricase from arthrobacter globiformis in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YZC
- Type
- protein
- Length
- 2,296 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uricase
- EC
- 1.7.3.3
- Ligands
- 1AL
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 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
- 1AL · Allantoate ion · 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 996 | 0.80 | 0.81 | 102 | 1AL |
| 2 | 1010 | 0.80 | 0.81 | 101 | 1AL |
| 3 | 893 | 0.77 | 0.79 | 80 | 1AL |
| 4 | 968 | 0.71 | 0.76 | 102 | empty |
| 5 | 644 | 0.71 | 0.78 | 60 | 1AL |
Interfaces
15 interfaces between chains.
- F–G · 3303 Ų buried · 57 hydrogen bonds · protein-protein
- B–C · 3291 Ų buried · 51 hydrogen bonds · protein-protein
- E–H · 3271 Ų buried · 52 hydrogen bonds · protein-protein
- A–D · 3242 Ų buried · 53 hydrogen bonds · protein-protein
- G–H · 2460 Ų buried · 54 hydrogen bonds · protein-protein
Compared structures
- 2YZC · Crystal structure of uricase from Arthrobacter globiformis in complex with allantoate · 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 2YZC · PDBe 2YZC
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