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The 2.14 a X-ray crystal structure of sporosarcina pasteurii urease in complex with AU(I) ions
Analyse The 2.14 a X-ray crystal structure of sporosarcina pasteurii urease in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6I9Y
- 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
- AU, NI, SO4, OH
- Pockets
- 4 · best druggability 0.71
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 | 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 | 28% helix, 22% strand | A0A0H3YL32 |
Ligands and binding sites
- AU · Gold ion · metal · 3 copies · chains C
- NI · Nickel (II) ion · metal · 2 copies · chains C
- SO4 · Sulfate ion · ion · 7 copies · chains A, C, B
- OH · Hydroxide ion · ion · chains C
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 693 | 0.71 | 0.78 | 63 | empty |
| 2 | 83 | 0.50 | 0.84 | 19 | OH, AU, SO4, EDO |
| 3 | 131 | 0.42 | 0.76 | 24 | empty |
| 4 | 122 | 0.39 | 0.75 | 18 | SO4 |
Interfaces
3 interfaces between chains.
- B–C · 1878 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 959 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 218 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (carboxylation).
Compared structures
- 6I9Y · The 2.14 A X-ray crystal structure of Sporosarcina pasteurii urease in complex with Au(I)… · 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 6I9Y · PDBe 6I9Y · UniProt A0A0H3YGY5 · UniProt P41021 · UniProt A0A0H3YL32
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