Research workbench
Crystal structure of klebsiella aerogenes urease, its apoenzyme and two active site mutants
Analyse Crystal structure of klebsiella aerogenes urease, its apoenzyme and two active… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KRB
- Type
- protein
- Length
- 767 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Urease
- EC
- 3.5.1.5
- UniProt
- P18316, P18315, P18314
- Ligands
- NI
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Urease (EC 3.5.1.5) | protein | 100 | 56% helix, 18% strand | P18316 |
| B | Urease (EC 3.5.1.5) | protein | 101 | 3% helix, 38% strand | P18315 |
| C | Urease (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
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 742 | 0.70 | 0.76 | 68 | empty |
| 2 | 179 | 0.43 | 0.74 | 30 | empty |
| 3 | 120 | 0.40 | 0.75 | 18 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1774 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 967 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 159 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 modified (carboxylation).
Compared structures
- 1KRB · Crystal structure of klebsiella aerogenes urease, its apoenzyme and two active site… · 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 1KRB · PDBe 1KRB · UniProt P18316 · UniProt P18315 · UniProt P18314
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