Research workbench
The crystal structure of sporosarcina pasteurii urease in complex with its substrate urea
Analyse The crystal structure of sporosarcina pasteurii urease in complex with its… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QDY
- 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
- A0A0H3YGY5, P41021, A0A0H3YL32
- Ligands
- URE, NI, SO4, F
- Pockets
- 2 · 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 | 56% helix, 18% strand | A0A0H3YGY5 |
| 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, 22% strand | A0A0H3YL32 |
Ligands and binding sites
- URE · Urea · ligand · chains C
- NI · Nickel (II) ion · metal · 2 copies · chains C
- SO4 · Sulfate ion · ion · 2 copies · chains B, C
- F · Fluoride ion · ion · chains C
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 840 | 0.72 | 0.77 | 85 | EDO |
| 2 | 108 | 0.37 | 0.74 | 18 | EDO |
Interfaces
3 interfaces between chains.
- B–C · 1859 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 918 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 224 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (carboxylation).
Compared structures
- 6QDY · The crystal structure of Sporosarcina pasteurii urease in complex with its substrate urea · the same entry in another collection · chain A against A, TM-score 1.00
- 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 A0A0H3YGY5
- Every structure of UniProt P41021
- Every structure of UniProt A0A0H3YL32
- Elsewhere: RCSB PDB 6QDY · PDBe 6QDY · UniProt A0A0H3YGY5 · UniProt P41021 · UniProt A0A0H3YL32
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