MolNFT v1 · #33054 · protein
Structure of protein TA0514, putative lipoate protein ligase from T. acidophilum with bound lipoic acid
2C8M · Lipoate-protein ligase a: “Structure of protein TA0514, putative lipoate protein ligase from T. acidophilum with bound lipoic acid”. X-ray diffraction, 1 ligand (LPA), 10 pockets (best druggability 0.84). MolNFT v1 #33054 on…
- 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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