Research workbench
3.0 a model of iron containing urease UREA2B2 from helicobacter mustelae (refined W/ no ordered solvent)
Analyse 3.0 a model of iron containing urease UREA2B2 from helicobacter mustelae… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QGK
- Type
- protein
- Length
- 4,734 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fusion of urease beta and gamma subunits; Urease subunit beta 2
- EC
- 3.5.1.5
- UniProt
- D3UJ81, D3UJ80
- Ligands
- FE
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, J, M, P | Fusion of urease beta and gamma subunits | protein | 225 | 32% helix, 25% strand | D3UJ81 |
| C, F, I, L, O, R | Urease subunit beta 2 (EC 3.5.1.5) | protein | 564 | 29% helix, 23% strand | D3UJ80 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 12 copies · chains C, F, I, L, O, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 989 | 0.84 | 0.85 | 85 | empty |
| 2 | 1012 | 0.83 | 0.84 | 101 | empty |
| 3 | 1070 | 0.82 | 0.83 | 99 | empty |
| 4 | 1071 | 0.82 | 0.83 | 106 | empty |
| 5 | 1116 | 0.82 | 0.83 | 106 | empty |
Interfaces
27 interfaces between chains.
- M–O · 2760 Ų buried · 46 hydrogen bonds · protein-protein
- J–L · 2753 Ų buried · 45 hydrogen bonds · protein-protein
- P–R · 2746 Ų buried · 48 hydrogen bonds · protein-protein
- G–I · 2743 Ų buried · 47 hydrogen bonds · protein-protein
- D–F · 2743 Ų buried · 45 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (carboxylation, formylation).
Compared structures
- 3QGK · 3.0 A Model of Iron Containing Urease UreA2B2 from Helicobacter mustelae (refined w/ no… · the same entry in another collection · chain J against J, 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 D3UJ81
- Every structure of UniProt D3UJ80
- Elsewhere: RCSB PDB 3QGK · PDBe 3QGK · UniProt D3UJ81 · UniProt D3UJ80
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