Research workbench
K217A variant of klebsiella aerogenes urease, chemically rescued by formate and nickel
Analyse K217A variant of klebsiella aerogenes urease, chemically rescued by formate and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1A5N
- Type
- protein
- Length
- 752 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Urease (gamma subunit); Urease (beta subunit); Urease (alpha subunit)
- EC
- 3.5.1.5
- UniProt
- P18316, P18315, P18314
- Ligands
- NI
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Urease (gamma subunit) (EC 3.5.1.5) | protein | 100 | 57% helix, 18% strand | P18316 |
| B | Urease (beta subunit) (EC 3.5.1.5) | protein | 101 | 3% helix, 38% strand | P18315 |
| C | Urease (alpha subunit) (EC 3.5.1.5) | protein | 551 | 29% helix, 24% strand | P18314 |
Ligands and binding sites
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 | 663 | 0.68 | 0.76 | 60 | empty |
| 2 | 123 | 0.41 | 0.76 | 17 | empty |
| 3 | 142 | 0.41 | 0.74 | 22 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1756 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 974 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 157 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1A5N · K217A variant of klebsiella aerogenes urease, chemically rescued by formate and nickel · 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 1.00
- 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 1A5N · PDBe 1A5N · UniProt P18316 · UniProt P18315 · UniProt P18314
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.