MolNFT v1 · #161914 · protein
Helicobacter pylori urease with bme bound in the active site
6QSU · Urease subunit alpha: “Helicobacter pylori urease with bme bound in the active site”. Electron microscopy, 1 ligand (NI), 20 pockets (best druggability 0.82). MolNFT v1 #161914 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6QSU
- 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
- 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 | 31% 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, 23% strand | A0A086RWB6 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 24 copies · chains B, J, D, F, H, L, N, P, R, T, V, X
- BME · Beta-mercaptoethanol · additive · 12 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 | 990 | 0.82 | 0.83 | 92 | BME |
| 2 | 1125 | 0.81 | 0.82 | 94 | BME |
| 3 | 1164 | 0.81 | 0.82 | 95 | BME |
| 4 | 1149 | 0.81 | 0.82 | 95 | BME |
| 5 | 1119 | 0.81 | 0.82 | 96 | BME |
Interfaces
78 interfaces between chains.
- W–X · 2734 Ų buried · 47 hydrogen bonds · protein-protein
- U–V · 2729 Ų buried · 50 hydrogen bonds · protein-protein
- Q–R · 2718 Ų buried · 45 hydrogen bonds · protein-protein
- G–H · 2717 Ų buried · 47 hydrogen bonds · protein-protein
- K–L · 2714 Ų buried · 43 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (carboxylation).
Compared structures
- 6QSU · Helicobacter pylori urease with BME 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 6QSU · PDBe 6QSU · UniProt A0A293SGE9 · UniProt A0A086RWB6
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