Research workbench
Crystal structure of lipoamide dehydrogenase from mycobacterium tuberculosis
Analyse Crystal structure of lipoamide dehydrogenase from mycobacterium tuberculosis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2A8X
- Type
- protein
- Length
- 928 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrolipoyl dehydrogenase
- EC
- 1.8.1.4
- UniProt
- P66004
- Ligands
- FAD
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dihydrolipoyl dehydrogenase (EC 1.8.1.4) | protein | 464 | 35% helix, 27% strand | P66004 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 975 | 0.82 | 0.83 | 98 | FAD |
| 2 | 944 | 0.81 | 0.82 | 88 | FAD |
| 3 | 120 | 0.78 | 0.97 | 33 | empty |
| 4 | 326 | 0.77 | 0.88 | 55 | empty |
| 5 | 170 | 0.72 | 0.90 | 35 | empty |
Interfaces
1 interface between chains.
- A–B · 3724 Ų buried · 57 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified, 2 disulfide (engineered, disulfide).
Compared structures
- 2A8X · Crystal Structure of Lipoamide Dehydrogenase from Mycobacterium tuberculosis · 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 P66004
- Elsewhere: RCSB PDB 2A8X · PDBe 2A8X · UniProt P66004
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