Research workbench
The crystal structure of urease from klebsiella aerogenes at 2.2 ångströms resolution
Analyse The crystal structure of urease from klebsiella aerogenes at 2.2 ångströms… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2KAU
- Type
- protein
- Length
- 767 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Urease (gamma chain); Urease (beta chain); Urease (alpha chain)
- EC
- 3.5.1.5
- UniProt
- P18316, P18315, P18314
- Ligands
- NI
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Urease (gamma chain) (EC 3.5.1.5) | protein | 100 | 56% helix, 18% strand | P18316 |
| B | Urease (beta chain) (EC 3.5.1.5) | protein | 101 | 3% helix, 38% strand | P18315 |
| C | Urease (alpha chain) (EC 3.5.1.5) | protein | 566 | 30% helix, 23% strand | P18314 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 2 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 650 | 0.68 | 0.76 | 54 | empty |
| 2 | 127 | 0.42 | 0.75 | 17 | empty |
| 3 | 149 | 0.41 | 0.74 | 22 | empty |
| 4 | 51 | 0.27 | 0.75 | 16 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1771 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 972 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 158 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 modified (carboxylation).
Compared structures
- 2KAU · The crystal structure of urease from klebsiella aerogenes at 2.2 ångströms resolution · the same entry in another collection · chain A against A, TM-score 1.00
- P18314 · AlphaFold monomer V2.0 prediction for urease subunit alpha (P18314) · a predicted model of the same protein · chain C against A, TM-score 0.99
- P18315 · AlphaFold monomer V2.0 prediction for urease subunit beta (P18315) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P18316 · AlphaFold monomer V2.0 prediction for urease subunit gamma (P18316) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P18316
- Every structure of UniProt P18315
- Every structure of UniProt P18314
- Elsewhere: RCSB PDB 2KAU · PDBe 2KAU · UniProt P18316 · UniProt P18315 · UniProt P18314
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