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Crystal structure of gamma-alpha subunit complex from burkholderia cepacia FAD glucose dehydrogenase
Analyse Crystal structure of gamma-alpha subunit complex from burkholderia cepacia FAD… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6A2U
- Type
- protein
- Length
- 1,288 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Twin-arginine translocation pathway signal; Glucose dehydrogenase
- EC
- 1.1.5.9
- UniProt
- Q8GQE7
- Ligands
- FAD, F3S
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Twin-arginine translocation pathway signal | protein | 114 | 48% helix, 4% strand | — |
| B, D | Glucose dehydrogenase (EC 1.1.5.9) | protein | 530 | 28% helix, 21% strand | Q8GQE7 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains B, D
- F3S · FE3-S4 cluster · ligand · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 702 | 0.83 | 0.86 | 75 | FAD |
| 2 | 713 | 0.83 | 0.86 | 75 | FAD |
| 3 | 1052 | 0.81 | 0.82 | 152 | empty |
| 4 | 62 | 0.68 | 0.95 | 19 | empty |
| 5 | 113 | 0.55 | 0.83 | 30 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1920 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1898 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 539 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 200 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 167 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor, 2 disulfide (flavinylation, disulfide).
Compared structures
- 6A2U · Crystal structure of gamma-alpha subunit complex from Burkholderia cepacia FAD glucose… · 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 Q8GQE7
- Elsewhere: RCSB PDB 6A2U · PDBe 6A2U · UniProt Q8GQE7
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