Research workbench
Biuret Hydrolase (BiuH) from Rhodococcus sp. Mel C169S bound with biuret
Analyse Biuret Hydrolase (BiuH) from Rhodococcus sp. Mel C169S bound with biuret in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XJM
- Type
- protein
- Length
- 911 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.05
- Source
- Rhodococcus sp. Mel
- Molecule
- Biuret hydrolase
- UniProt
- H8ZKV9
- Ligands
- C5J
- Pockets
- 5 · best druggability 0.87
Structure
x-ray diffraction · resolution 2.05 · 4 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Biuret hydrolase | protein | 226 | 40% helix, 22% strand | H8ZKV9 |
| B | Biuret hydrolase | protein | 227 | 38% helix, 19% strand | H8ZKV9 |
| C | Biuret hydrolase | protein | 228 | 38% helix, 22% strand | H8ZKV9 |
| D | Biuret hydrolase | protein | 230 | 39% helix, 20% strand | H8ZKV9 |
Ligands and binding sites
- C5J · dicarbonimidic diamide · ligand · 4 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 513 | 0.87 | 0.94 | 44 | empty |
| 2 | 286 | 0.61 | 0.80 | 33 | empty |
| 3 | 282 | 0.61 | 0.79 | 34 | empty |
| 4 | 282 | 0.60 | 0.79 | 33 | empty |
| 5 | 316 | 0.59 | 0.77 | 36 | empty |
Interfaces
6 interfaces between chains.
- B–C · 2019 Ų buried · 40 hydrogen bonds · protein-protein
- A–D · 2009 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 858 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 846 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 234 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6XJM · Biuret hydrolase (biuh) from rhodococcus sp. mel C169S bound with biuret · 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 H8ZKV9
- Elsewhere: RCSB PDB 6XJM · PDBe 6XJM · UniProt H8ZKV9
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