Research workbench
Crystal structure of the putative glutaryl-CoA dehydrogenase from thermus thermophilus
Analyse Crystal structure of the putative glutaryl-CoA dehydrogenase from thermus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2EBA
- Type
- protein
- Length
- 3,040 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative glutaryl-CoA dehydrogenase
- EC
- 1.3.99.7
- UniProt
- Q5SK63
- Ligands
- FAD
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 57% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E, F, G, H, I | Putative glutaryl-CoA dehydrogenase (EC 1.3.99.7) | protein | 380 | 57% helix, 14% strand | Q5SK63 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 8 copies · chains A, C, D, E, F, G, I, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 601 | 0.84 | 0.89 | 79 | FAD |
| 2 | 625 | 0.84 | 0.89 | 76 | FAD |
| 3 | 612 | 0.84 | 0.89 | 77 | FAD |
| 4 | 564 | 0.84 | 0.89 | 72 | FAD |
| 5 | 606 | 0.84 | 0.88 | 74 | FAD |
Interfaces
13 interfaces between chains.
- A–C · 2078 Ų buried · 26 hydrogen bonds · protein-protein
- F–I · 2075 Ų buried · 31 hydrogen bonds · protein-protein
- G–H · 2075 Ų buried · 29 hydrogen bonds · protein-protein
- C–E · 2053 Ų buried · 35 hydrogen bonds · protein-protein
- D–E · 2039 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 2EBA · Crystal structure of the putative glutaryl-CoA dehydrogenase from thermus thermophilus · 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 Q5SK63
- Elsewhere: RCSB PDB 2EBA · PDBe 2EBA · UniProt Q5SK63
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