Research workbench
Crystal structure of Arginase from Bacillus cereus
Analyse Crystal structure of Arginase from Bacillus cereus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NBK
- Type
- protein
- Length
- 1,726 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.91
- Source
- Bacillus thuringiensis DB27
- Molecule
- Arginase
- EC
- 3.5.3.1
- UniProt
- W8YSI5
- Ligands
- MN, CA
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · resolution 1.91 · 6 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Arginase (EC 3.5.3.1) | protein | 289 | 43% helix, 19% strand | W8YSI5 |
| B | Arginase (EC 3.5.3.1) | protein | 287 | 43% helix, 19% strand | W8YSI5 |
| C | Arginase (EC 3.5.3.1) | protein | 286 | 43% helix, 19% strand | W8YSI5 |
| D | Arginase (EC 3.5.3.1) | protein | 287 | 44% helix, 19% strand | W8YSI5 |
| E | Arginase (EC 3.5.3.1) | protein | 288 | 43% helix, 19% strand | W8YSI5 |
| F | Arginase (EC 3.5.3.1) | protein | 289 | 43% helix, 19% strand | W8YSI5 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 14 copies · chains A, B, C, D, E, F
- CA · Calcium ion · metal · 3 copies · chains A, D, B, F, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1176 | 0.81 | 0.82 | 88 | empty |
| 2 | 1124 | 0.80 | 0.82 | 82 | CA |
| 3 | 487 | 0.70 | 0.80 | 39 | empty |
| 4 | 526 | 0.69 | 0.79 | 43 | empty |
| 5 | 520 | 0.68 | 0.79 | 46 | empty |
Interfaces
12 interfaces between chains.
- D–F · 753 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 729 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 725 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 707 Ų buried · 10 hydrogen bonds · protein-protein
- B–F · 703 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6NBK · Crystal structure of arginase from bacillus cereus · 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 W8YSI5
- Elsewhere: RCSB PDB 6NBK · PDBe 6NBK · UniProt W8YSI5
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