Research workbench
Granulibacter bethesdensis allophanate hydrolase co-crystallized with malonate
Analyse Granulibacter bethesdensis allophanate hydrolase co-crystallized with malonate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GYS
- Type
- protein
- Length
- 921 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.201
- Source
- Granulibacter bethesdensis
- Molecule
- Allophanate hydrolase
- EC
- 3.5.1.54
- UniProt
- Q0BRB0
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · resolution 2.201 · 2 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Allophanate hydrolase (EC 3.5.1.54) | protein | 460 | 39% helix, 18% strand | Q0BRB0 |
| B | Allophanate hydrolase (EC 3.5.1.54) | protein | 461 | 40% helix, 18% strand | Q0BRB0 |
Ligands and binding sites
- MLI · Malonate ion · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1064 | 0.75 | 0.77 | 76 | empty |
| 2 | 52 | 0.52 | 0.87 | 15 | empty |
| 3 | 54 | 0.49 | 0.85 | 13 | empty |
| 4 | 103 | 0.46 | 0.80 | 31 | MLI |
| 5 | 70 | 0.38 | 0.79 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1168 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 4GYS · Granulibacter bethesdensis allophanate hydrolase co-crystallized with malonate · 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 Q0BRB0
- Elsewhere: RCSB PDB 4GYS · PDBe 4GYS · UniProt Q0BRB0
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