Research workbench
Helicobacter pylori urease with inhibitor bound in the active site
Analyse Helicobacter pylori urease with inhibitor bound in the active site in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZJA
- Type
- protein
- Length
- 9,684 residues
- Chains
- 24
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Urease subunit alpha; Urease subunit beta
- EC
- 3.5.1.5
- UniProt
- A0A293SGE9, A0A086RWB6
- Ligands
- DJM, NI
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 2 distinct chains · 30% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K, M, O, Q, S, U, W | Urease subunit alpha (EC 3.5.1.5) | protein | 238 | 32% helix, 24% strand | A0A293SGE9 |
| B, J, D, F, H, L, N, P, R, T, V, X | Urease subunit beta (EC 3.5.1.5) | protein | 569 | 30% helix, 22% strand | A0A086RWB6 |
Ligands and binding sites
- DJM · 2-{[1-(3,5-dimethylphenyl)-1H-imidazol-2-yl]sulfanyl}-N-hydroxyacetamide · ligand · 12 copies · chains B, R, J, L, D, X, F, V, H, T, N, P
- NI · Nickel (II) ion · metal · 24 copies · chains B, J, D, F, H, L, N, P, R, T, V, X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1038 | 0.82 | 0.83 | 94 | NI, DJM |
| 2 | 1018 | 0.82 | 0.83 | 97 | DJM |
| 3 | 1002 | 0.82 | 0.83 | 88 | DJM |
| 4 | 965 | 0.82 | 0.83 | 84 | NI, DJM |
| 5 | 1020 | 0.82 | 0.83 | 91 | NI, DJM |
Interfaces
78 interfaces between chains.
- O–P · 2753 Ų buried · 41 hydrogen bonds · protein-protein
- K–L · 2743 Ų buried · 41 hydrogen bonds · protein-protein
- S–T · 2738 Ų buried · 39 hydrogen bonds · protein-protein
- W–X · 2733 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 2733 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (carboxylation).
Compared structures
- 6ZJA · Helicobacter pylori urease with inhibitor bound in the active site · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A293SGE9
- Every structure of UniProt A0A086RWB6
- Elsewhere: RCSB PDB 6ZJA · PDBe 6ZJA · UniProt A0A293SGE9 · UniProt A0A086RWB6
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