Research workbench
Crystal structure of enterococcus faecalis lipoate-protein ligase a (lpla-2) in complex with lipoyl-AMP
Analyse Crystal structure of enterococcus faecalis lipoate-protein ligase a (lpla-2) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ICL
- Type
- protein
- Length
- 641 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipoate--protein ligase
- EC
- 2.7.7.63
- UniProt
- Q830N7
- Ligands
- LAQ
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lipoate--protein ligase (EC 2.7.7.63) | protein | 320 | 36% helix, 26% strand | Q830N7 |
| B | Lipoate--protein ligase (EC 2.7.7.63) | protein | 321 | 36% helix, 27% strand | Q830N7 |
Ligands and binding sites
- LAQ · 5'-O-[(R)-({5-[(3R)-1,2-dithiolan-3-yl]pentanoyl}oxy) (hydroxy)phosphoryl]adenosine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 331 | 0.65 | 0.80 | 57 | LAQ |
| 2 | 293 | 0.64 | 0.81 | 56 | LAQ |
| 3 | 176 | 0.51 | 0.78 | 21 | empty |
| 4 | 160 | 0.47 | 0.76 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 77 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5ICL · Crystal structure of Enterococcus faecalis lipoate-protein ligase A (lplA-2) in complex… · 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 Q830N7
- Elsewhere: RCSB PDB 5ICL · PDBe 5ICL · UniProt Q830N7
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