MolNFT v1 · #82491 · protein
Crystal structure of L-amino acid ligase from bacillus licheniformis
3VOT · L-amino acid ligase, BL00235: “Crystal structure of L-amino acid ligase from bacillus licheniformis”. X-ray diffraction, 3 ligands (ADP, CA, CL), 7 pockets (best druggability 0.81). MolNFT v1 #82491 on GenesisL1: 3D structure…
- PDB
- 3VOT
- Type
- protein
- Length
- 805 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-amino acid ligase, BL00235
- EC
- 6.3.2.28
- UniProt
- Q65D11
- Ligands
- ADP, CA, CL
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-amino acid ligase, BL00235 (EC 6.3.2.28) | protein | 411 | 34% helix, 27% strand | Q65D11 |
| B | L-amino acid ligase, BL00235 (EC 6.3.2.28) | protein | 394 | 31% helix, 28% strand | Q65D11 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 9 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 829 | 0.81 | 0.84 | 70 | empty |
| 2 | 1100 | 0.75 | 0.78 | 106 | empty |
| 3 | 777 | 0.73 | 0.78 | 80 | ADP, CA, CL |
| 4 | 715 | 0.72 | 0.78 | 67 | ADP, CA |
| 5 | 167 | 0.47 | 0.76 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 470 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3VOT · Crystal structure of L-amino acid ligase from Bacillus licheniformis · 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 Q65D11
- Elsewhere: RCSB PDB 3VOT · PDBe 3VOT · UniProt Q65D11
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