Research workbench
Crystal structure of aspartase from bacillus sp. YM55-1 with bound L- aspartate
Analyse Crystal structure of aspartase from bacillus sp. YM55-1 with bound L- aspartate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3R6V
- Type
- protein
- Length
- 3,683 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
- ASP, CA
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 60% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aspartase (EC 4.3.1.1) | protein | 458 | 58% helix, 7% strand | Q9LCC6 |
| B, C | Aspartase (EC 4.3.1.1) | protein | 462 | 60% helix, 7% strand | Q9LCC6 |
| D, E, H | Aspartase (EC 4.3.1.1) | protein | 459 | 61% helix, 7% strand | Q9LCC6 |
| F | Aspartase (EC 4.3.1.1) | protein | 461 | 61% helix, 7% strand | Q9LCC6 |
| G | Aspartase (EC 4.3.1.1) | protein | 463 | 60% helix, 8% strand | Q9LCC6 |
Ligands and binding sites
- ASP · Aspartic acid · ligand · 2 copies · chains A, B, C, E, F, G
- 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 | 1109 | 0.81 | 0.83 | 91 | empty |
| 2 | 140 | 0.81 | 0.98 | 36 | empty |
| 3 | 108 | 0.78 | 0.98 | 30 | empty |
| 4 | 745 | 0.77 | 0.81 | 66 | empty |
| 5 | 107 | 0.77 | 0.97 | 26 | empty |
Interfaces
14 interfaces between chains.
- E–F · 3431 Ų buried · 54 hydrogen bonds · protein-protein
- A–B · 3408 Ų buried · 49 hydrogen bonds · protein-protein
- G–H · 3406 Ų buried · 55 hydrogen bonds · protein-protein
- C–D · 3397 Ų buried · 56 hydrogen bonds · protein-protein
- B–C · 2562 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 3R6V · Crystal structure of aspartase from Bacillus sp. YM55-1 with bound L-aspartate · the same entry in another collection · chain B against B, 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 3R6V · PDBe 3R6V · UniProt Q9LCC6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.