Research workbench
The first jack bean urease (canavalia ensiformis) complex obtained at 1.52 resolution
Analyse The first jack bean urease (canavalia ensiformis) complex obtained at 1.52… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4H9M
- 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
- HAE, NI
- Pockets
- 5 · 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
- HAE · Acetohydroxamic acid · ligand · chains A
- NI · Nickel (II) ion · metal · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 29 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 962 | 0.72 | 0.76 | 96 | EDO |
| 2 | 97 | 0.47 | 0.81 | 21 | NI, EDO, HAE |
| 3 | 137 | 0.42 | 0.75 | 16 | EDO |
| 4 | 83 | 0.32 | 0.73 | 16 | EDO |
| 5 | 72 | 0.31 | 0.74 | 16 | EDO |
Modifications
Observed in the structure: 8 modified (artifact, carboxylation).
Compared structures
- 4H9M · The first Jack bean urease (Canavalia ensiformis) complex obtained at 1.52 resolution · 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 4H9M · PDBe 4H9M · UniProt P07374
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