Research workbench
Crystal structure of helicobacter pylori urease in complex with acetohydroxamic acid
Analyse Crystal structure of helicobacter pylori urease in complex with acetohydroxamic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1E9Y
- Type
- protein
- Length
- 807 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Urease subunit alpha; Urease subunit beta
- EC
- 3.5.1.5
- UniProt
- P14916, P69996
- Ligands
- HAE, NI
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Urease subunit alpha (EC 3.5.1.5) | protein | 238 | 31% helix, 23% strand | P14916 |
| B | Urease subunit beta (EC 3.5.1.5) | protein | 569 | 28% helix, 22% strand | P69996 |
Ligands and binding sites
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 | 770 | 0.70 | 0.76 | 85 | empty |
| 2 | 85 | 0.47 | 0.82 | 23 | HAE, NI |
| 3 | 124 | 0.43 | 0.76 | 17 | empty |
| 4 | 66 | 0.34 | 0.76 | 17 | empty |
| 5 | 78 | 0.33 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2728 Ų buried · 39 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (carboxylation).
Compared structures
- 1E9Y · Crystal structure of Helicobacter pylori urease in complex with acetohydroxamic acid · the same entry in another collection · chain A against A, TM-score 1.00
- P69996 · AlphaFold monomer V2.0 prediction for urease subunit beta (P69996) · a predicted model of the same protein · chain B against A, TM-score 1.00
- P14916 · AlphaFold monomer V2.0 prediction for urease subunit alpha (P14916) · 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 P14916
- Every structure of UniProt P69996
- Elsewhere: RCSB PDB 1E9Y · PDBe 1E9Y · UniProt P14916 · UniProt P69996
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