Research workbench
2.07 a resolution 1,4-benzoquinone inhibited sporosarcina pasteurii urease
Analyse 2.07 a resolution 1,4-benzoquinone inhibited sporosarcina pasteurii urease in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FSE
- Type
- protein
- Length
- 792 residues
- Chains
- 3
- 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
- P41022, P41021, P41020
- Ligands
- HQE, NI, SO4, OH
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Urease subunit gamma (EC 3.5.1.5) | protein | 100 | 55% helix, 18% strand | P41022 |
| B | Urease subunit beta (EC 3.5.1.5) | protein | 122 | 15% helix, 31% strand | P41021 |
| C | Urease subunit alpha (EC 3.5.1.5) | protein | 570 | 29% helix, 23% strand | P41020 |
Ligands and binding sites
- HQE · benzene-1,4-diol · ligand · 2 copies · chains C
- NI · Nickel (II) ion · metal · 2 copies · chains C
- SO4 · Sulfate ion · ion · 9 copies · chains A, C, B
- OH · Hydroxide ion · ion · chains C
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B, 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 | 892 | 0.72 | 0.77 | 91 | empty |
| 2 | 132 | 0.49 | 0.79 | 26 | NI, SO4, OH |
| 3 | 107 | 0.38 | 0.75 | 17 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1853 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 942 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 219 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, carboxylation).
Compared structures
- 5FSE · 2.07 A resolution 1,4-Benzoqui inhibited Sporosarcina pasteurii urease · the same entry in another collection · chain C against C, TM-score 1.00
- P41020 · AlphaFold monomer V2.0 prediction for urease subunit alpha (P41020) · a predicted model of the same protein · chain C against A, TM-score 0.99
- P41022 · AlphaFold monomer V2.0 prediction for urease subunit gamma (P41022) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P41021 · AlphaFold monomer V2.0 prediction for urease subunit beta (P41021) · a predicted model of the same protein · chain B 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 P41022
- Every structure of UniProt P41021
- Every structure of UniProt P41020
- Elsewhere: RCSB PDB 5FSE · PDBe 5FSE · UniProt P41022 · UniProt P41021 · UniProt P41020
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