Research workbench
Structure of protein TA0514, putative lipoate protein ligase from T. acidophilum with bound lipoic acid
Analyse Structure of protein TA0514, putative lipoate protein ligase from T.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2C8M
- Type
- protein
- Length
- 972 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipoate-protein ligase a
- EC
- 6.3.2.-
- UniProt
- Q9HKT1
- Ligands
- LPA
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lipoate-protein ligase a (EC 6.3.2.-) | protein | 241 | 37% helix, 26% strand | Q9HKT1 |
| B, C | Lipoate-protein ligase a (EC 6.3.2.-) | protein | 245 | 37% helix, 27% strand | Q9HKT1 |
| D | Lipoate-protein ligase a (EC 6.3.2.-) | protein | 241 | 37% helix, 27% strand | Q9HKT1 |
Ligands and binding sites
- LPA · Lipoic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1042 | 0.84 | 0.85 | 139 | LPA |
| 2 | 385 | 0.69 | 0.82 | 55 | LPA |
| 3 | 629 | 0.69 | 0.78 | 77 | empty |
| 4 | 219 | 0.68 | 0.85 | 38 | LPA |
| 5 | 155 | 0.56 | 0.81 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–C · 573 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 548 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 425 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2C8M · Structure of protein Ta0514, putative lipoate protein ligase from T. acidophilum with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9HKT1 · AlphaFold monomer V2.0 prediction for lipoate-protein ligase a subunit 1 (Q9HKT1) · a predicted model of the same protein · chain D against A, TM-score 0.97
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 Q9HKT1
- Elsewhere: RCSB PDB 2C8M · PDBe 2C8M · UniProt Q9HKT1
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