Research workbench
Crystal structure of urease from yersinia enterocolitica
Analyse Crystal structure of urease from yersinia enterocolitica in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Z42
- Type
- protein
- Length
- 3,136 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Urease subunit gamma; Urease subunit beta; Urease subunit alpha
- EC
- 3.5.1.5
- UniProt
- F4MWM9, F4MWM8, F4MWM7
- Ligands
- NI
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 26% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, J | Urease subunit gamma (EC 3.5.1.5) | protein | 99 | 49% helix, 12% strand | F4MWM9 |
| B, E, H, K | Urease subunit beta (EC 3.5.1.5) | protein | 114 | 6% helix, 30% strand | F4MWM8 |
| C, F, I, L | Urease subunit alpha (EC 3.5.1.5) | protein | 571 | 26% helix, 20% strand | F4MWM7 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 8 copies · chains C, F, I, L
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 | 882 | 0.79 | 0.82 | 71 | empty |
| 2 | 849 | 0.79 | 0.82 | 72 | empty |
| 3 | 872 | 0.78 | 0.81 | 69 | empty |
| 4 | 409 | 0.77 | 0.86 | 40 | empty |
| 5 | 576 | 0.74 | 0.81 | 47 | empty |
Interfaces
27 interfaces between chains.
- C–F · 2573 Ų buried · 37 hydrogen bonds · protein-protein
- F–I · 2572 Ų buried · 36 hydrogen bonds · protein-protein
- C–I · 2567 Ų buried · 41 hydrogen bonds · protein-protein
- E–F · 1704 Ų buried · 23 hydrogen bonds · protein-protein
- H–I · 1697 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 4Z42 · Crystal structure of urease from Yersinia enterocolitica · 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 F4MWM9
- Every structure of UniProt F4MWM8
- Every structure of UniProt F4MWM7
- Elsewhere: RCSB PDB 4Z42 · PDBe 4Z42 · UniProt F4MWM9 · UniProt F4MWM8 · UniProt F4MWM7
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