Research workbench
A triclinic-lattice structure of aspartase from bacillus sp. YM55-1
Analyse A triclinic-lattice structure of 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
- 3R6Q
- Type
- protein
- Length
- 3,697 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 0.81
Structure
x-ray diffraction · 2 distinct chains · 61% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, G, H | Aspartase (EC 4.3.1.1) | protein | 462 | 61% helix, 7% strand | Q9LCC6 |
| F | Aspartase (EC 4.3.1.1) | protein | 463 | 60% helix, 8% strand | Q9LCC6 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, D, E, H
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 | 654 | 0.81 | 0.86 | 61 | empty |
| 2 | 730 | 0.78 | 0.83 | 59 | empty |
| 3 | 112 | 0.78 | 0.98 | 27 | empty |
| 4 | 781 | 0.78 | 0.82 | 61 | empty |
| 5 | 871 | 0.77 | 0.80 | 61 | empty |
Interfaces
15 interfaces between chains.
- E–F · 3476 Ų buried · 51 hydrogen bonds · protein-protein
- G–H · 3475 Ų buried · 50 hydrogen bonds · protein-protein
- C–D · 3466 Ų buried · 55 hydrogen bonds · protein-protein
- A–B · 3453 Ų buried · 50 hydrogen bonds · protein-protein
- F–G · 2300 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 3R6Q · A triclinic-lattice structure of 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 3R6Q · PDBe 3R6Q · UniProt Q9LCC6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.