Research workbench
Crystal structure of bacillus megaterium glucose dehydrogenase 4 A258F mutant in complex with NADH and D-glucose
Analyse Crystal structure of bacillus megaterium glucose dehydrogenase 4 A258F mutant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3AY6
- Type
- protein
- Length
- 1,059 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucose 1-dehydrogenase 4
- EC
- 1.1.1.47
- UniProt
- P39485
- Ligands
- NAI, BGC, CL
- Pockets
- 9 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 54% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucose 1-dehydrogenase 4 (EC 1.1.1.47) | protein | 263 | 54% helix, 14% strand | P39485 |
| B, D | Glucose 1-dehydrogenase 4 (EC 1.1.1.47) | protein | 267 | 54% helix, 14% strand | P39485 |
| C | Glucose 1-dehydrogenase 4 (EC 1.1.1.47) | protein | 262 | 55% helix, 15% strand | P39485 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- BGC · beta-D-glucopyranose · sugar · 4 copies · chains A, C, B, D
- CL · Chloride ion · ion · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 549 | 0.86 | 0.92 | 53 | empty |
| 2 | 377 | 0.73 | 0.84 | 46 | BGC, NAI |
| 3 | 369 | 0.72 | 0.84 | 44 | NAI, BGC |
| 4 | 363 | 0.72 | 0.84 | 46 | NAI, BGC |
| 5 | 368 | 0.71 | 0.83 | 43 | BGC, NAI |
Interfaces
6 interfaces between chains.
- A–D · 1733 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1686 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1607 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1597 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1147 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 3AY6 · Crystal structure of Bacillus megaterium glucose dehydrogenase 4 A258F mutant in complex… · the same entry in another collection · chain D against D, TM-score 1.00
- P39485 · AlphaFold monomer V2.0 prediction for glucose 1-dehydrogenase 4 (P39485) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 P39485
- Elsewhere: RCSB PDB 3AY6 · PDBe 3AY6 · UniProt P39485
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