Research workbench
BD2924 apo-form
Analyse BD2924 apo-form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SD8
- Type
- protein
- Length
- 1,006 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable acyl-CoA dehydrogenase
- EC
- 1.3.99.-
- UniProt
- Q6MJ59
- Ligands
- FAD
- Pockets
- 11 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 57% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X, A | Probable acyl-CoA dehydrogenase (EC 1.3.99.-) | protein | 503 | 57% helix, 14% strand | Q6MJ59 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains X, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1105 | 0.84 | 0.85 | 115 | FAD |
| 2 | 1158 | 0.82 | 0.83 | 101 | FAD |
| 3 | 409 | 0.61 | 0.76 | 39 | empty |
| 4 | 172 | 0.57 | 0.81 | 33 | empty |
| 5 | 112 | 0.54 | 0.83 | 20 | empty |
Interfaces
1 interface between chains.
- X–A · 2639 Ų buried · 43 hydrogen bonds · protein-protein
Compared structures
- 6SD8 · Bd2924 apo-form · the same entry in another collection · chain X against X, 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 Q6MJ59
- Elsewhere: RCSB PDB 6SD8 · PDBe 6SD8 · UniProt Q6MJ59
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