MolNFT v1 · #93296 · protein
Crystallographic structure analysis of urease from jack bean (canavalia ensiformis) at 1.49 a resolution
4GY7: “Crystallographic structure analysis of urease from jack bean (canavalia ensiformis) at 1.49 a resolution”. X-ray diffraction, 4 ligands (ACN, NI, NA), 4 pockets (best druggability 0.72). MolNFT v1 #93296 on GenesisL1: 3D structure…
- PDB
- 4GY7
- Type
- protein
- Length
- 836 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Urease
- EC
- 3.5.1.5
- UniProt
- P07374
- Ligands
- ACN, NI, NA, PO4
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Urease (EC 3.5.1.5) | protein | 836 | 30% helix, 23% strand | P07374 |
Ligands and binding sites
- ACN · Acetone · ligand · 5 copies · chains A
- NI · Nickel (II) ion · metal · 2 copies · chains A
- NA · Sodium ion · metal · 2 copies · chains A
- PO4 · Phosphate ion · ion · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 13 copies · chains A
- BME · Beta-mercaptoethanol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 942 | 0.72 | 0.76 | 100 | empty |
| 2 | 139 | 0.42 | 0.75 | 17 | empty |
| 3 | 78 | 0.30 | 0.73 | 15 | empty |
| 4 | 64 | 0.29 | 0.74 | 17 | empty |
Modifications
Observed in the structure: 9 modified (artifact, carboxylation).
Compared structures
- 4GY7 · Crystallographic structure analysis of urease from Jack bean (Canavalia ensiformis) at… · the same entry in another collection · chain A against A, TM-score 1.00
- P07374 · AlphaFold monomer V2.0 prediction for urease (P07374) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P07374
- Elsewhere: RCSB PDB 4GY7 · PDBe 4GY7 · UniProt P07374
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