Research workbench
Crystal structure of lipoate protein ligase from mycoplasma hyopneumoniae
Analyse Crystal structure of lipoate protein ligase from mycoplasma hyopneumoniae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JOM
- Type
- protein
- Length
- 661 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipoate--protein ligase
- EC
- 6.3.1.20
- UniProt
- Q4AA29
- Ligands
- LAQ
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lipoate--protein ligase (EC 6.3.1.20) | protein | 331 | 36% helix, 27% strand | Q4AA29 |
| B | Lipoate--protein ligase (EC 6.3.1.20) | protein | 330 | 36% helix, 26% strand | Q4AA29 |
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
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1121 | 0.74 | 0.77 | 101 | LAQ |
| 2 | 673 | 0.70 | 0.78 | 90 | LAQ |
| 3 | 115 | 0.39 | 0.74 | 18 | empty |
| 4 | 86 | 0.38 | 0.76 | 17 | empty |
| 5 | 67 | 0.34 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 255 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6JOM · Crystal structure of lipoate protein ligase from Mycoplasma hyopneumoniae · 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 Q4AA29
- Elsewhere: RCSB PDB 6JOM · PDBe 6JOM · UniProt Q4AA29
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