MolNFT v1 · #161416 · protein
The crystal structure of sporosarcina pasteurii urease in complex with its substrate urea
6QDY · Urease subunit gamma: “The crystal structure of sporosarcina pasteurii urease in complex with its substrate urea”. X-ray diffraction, 4 ligands (URE, NI, SO4), 2 pockets (best druggability 0.72). MolNFT v1 #161416 on GenesisL1: 3D…
- 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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