Research workbench
Crystal structure of a glutaryl-CoA dehydrogenase from mycobacterium smegmatis in complex with FADH2
Analyse Crystal structure of a glutaryl-CoA dehydrogenase from mycobacterium smegmatis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SWO
- Type
- protein
- Length
- 1,546 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutaryl-CoA dehydrogenase
- EC
- 1.3.99.7
- UniProt
- A0R6V6
- Ligands
- FDA, UNX
- Pockets
- 16 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 58% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutaryl-CoA dehydrogenase (EC 1.3.99.7) | protein | 388 | 57% helix, 15% strand | A0R6V6 |
| B, C, D | Glutaryl-CoA dehydrogenase (EC 1.3.99.7) | protein | 386 | 58% helix, 15% strand | A0R6V6 |
Ligands and binding sites
- FDA · Dihydroflavine-adenine dinucleotide · ligand · 4 copies · chains A, C, D, B
- UNX · Unknown atom or ion · ion · 15 copies · chains C, D
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 628 | 0.83 | 0.88 | 69 | FDA, EDO |
| 2 | 627 | 0.83 | 0.88 | 69 | FDA, EDO |
| 3 | 649 | 0.83 | 0.87 | 74 | FDA, EDO |
| 4 | 662 | 0.83 | 0.87 | 73 | FDA, EDO |
| 5 | 522 | 0.72 | 0.81 | 62 | empty |
Interfaces
6 interfaces between chains.
- A–C · 2266 Ų buried · 30 hydrogen bonds · protein-protein
- B–D · 2262 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 2220 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 2203 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 252 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3SWO · Crystal structure of a glutaryl-coa dehydrogenase from mycobacterium smegmatis in complex… · 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 A0R6V6
- Elsewhere: RCSB PDB 3SWO · PDBe 3SWO · UniProt A0R6V6
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