Research workbench
1.65 A resolution 4,5-dimethylcatechol (4,5-dimethylbenzene-1,2-diol) inhibited Sporosarcina pasteurii urease
Analyse 1.65 A resolution 4,5-dimethylcatechol (4,5-dimethylbenzene-1,2-diol) inhibited… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZO2
- Type
- protein
- Length
- 792 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.65
- Source
- Sporosarcina pasteurii
- Molecule
- Urease subunit gamma; Urease subunit beta; Urease subunit alpha
- EC
- 3.5.1.5
- UniProt
- A0A0H3YGY5, P41021, A0A0H3YL32
- Ligands
- NI, SO4, OH
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · resolution 1.65 · 3 distinct chains · 30% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| AAA | Urease subunit gamma (EC 3.5.1.5) | protein | 100 | 55% helix, 18% strand | A0A0H3YGY5 |
| BBB | Urease subunit beta (EC 3.5.1.5) | protein | 122 | 15% helix, 31% strand | P41021 |
| CCC | Urease subunit alpha (EC 3.5.1.5) | protein | 570 | 28% helix, 23% strand | A0A0H3YL32 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 2 copies · chains CCC
- SO4 · Sulfate ion · ion · 11 copies · chains AAA, CCC, BBB
- OH · Hydroxide ion · ion · chains CCC
- EDO · 1,2-ethanediol · additive · 24 copies · chains AAA, CCC, BBB
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 843 | 0.72 | 0.77 | 91 | empty |
| 2 | 112 | 0.54 | 0.83 | 20 | OH, EDO, SO4 |
| 3 | 103 | 0.37 | 0.75 | 17 | EDO |
Interfaces
3 interfaces between chains.
- BBB–CCC · 1875 Ų buried · 34 hydrogen bonds · protein-protein
- AAA–CCC · 947 Ų buried · 14 hydrogen bonds · protein-protein
- AAA–BBB · 221 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (carboxylation, nonstandard).
Compared structures
- P41021 · AlphaFold monomer V2.0 prediction for urease subunit beta (P41021) · a predicted model of the same protein · chain BBB 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 A0A0H3YGY5
- Every structure of UniProt P41021
- Every structure of UniProt A0A0H3YL32
- Elsewhere: RCSB PDB 6ZO2 · PDBe 6ZO2 · UniProt A0A0H3YGY5 · UniProt P41021 · UniProt A0A0H3YL32
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.