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Crystal structure of chymotrypsin-treated aspartase from bacillus sp. YM55-1
Analyse Crystal structure of chymotrypsin-treated aspartase from bacillus sp. YM55-1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3R6Y
- Type
- protein
- Length
- 3,108 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartase
- EC
- 4.3.1.1
- UniProt
- Q9LCC6
- Ligands
- CA
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 59% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, F, H | Aspartase (EC 4.3.1.1) | protein | 390 | 59% helix, 7% strand | Q9LCC6 |
| C | Aspartase (EC 4.3.1.1) | protein | 383 | 60% helix, 7% strand | Q9LCC6 |
| E | Aspartase (EC 4.3.1.1) | protein | 391 | 58% helix, 7% strand | Q9LCC6 |
| G | Aspartase (EC 4.3.1.1) | protein | 384 | 60% helix, 7% strand | Q9LCC6 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains B, C, F, G
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 | 123 | 0.80 | 0.98 | 27 | empty |
| 2 | 119 | 0.79 | 0.97 | 27 | empty |
| 3 | 760 | 0.75 | 0.80 | 71 | empty |
| 4 | 72 | 0.74 | 0.98 | 22 | empty |
| 5 | 70 | 0.74 | 0.98 | 18 | empty |
Interfaces
19 interfaces between chains.
- E–F · 2862 Ų buried · 48 hydrogen bonds · protein-protein
- C–D · 2846 Ų buried · 50 hydrogen bonds · protein-protein
- A–B · 2845 Ų buried · 48 hydrogen bonds · protein-protein
- G–H · 2837 Ų buried · 46 hydrogen bonds · protein-protein
- A–D · 2768 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 3R6Y · Crystal structure of chymotrypsin-treated aspartase from Bacillus sp. YM55-1 · 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 Q9LCC6
- Elsewhere: RCSB PDB 3R6Y · PDBe 3R6Y · UniProt Q9LCC6
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