Research workbench
Pyranose 2-oxidase Y456W mutant in complex with 2FG
Analyse Pyranose 2-oxidase Y456W mutant in complex with 2FG in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3K4M
- Type
- protein
- Length
- 4,594 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyranose 2-oxidase
- EC
- 1.1.3.10
- UniProt
- Q7ZA32
- Ligands
- FAD, SHG
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 5 distinct chains · 25% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyranose 2-oxidase (EC 1.1.3.10) | protein | 574 | 25% helix, 24% strand | Q7ZA32 |
| B | Pyranose 2-oxidase (EC 1.1.3.10) | protein | 577 | 25% helix, 24% strand | Q7ZA32 |
| C, D | Pyranose 2-oxidase (EC 1.1.3.10) | protein | 574 | 25% helix, 24% strand | Q7ZA32 |
| E | Pyranose 2-oxidase (EC 1.1.3.10) | protein | 576 | 25% helix, 23% strand | Q7ZA32 |
| F, G, H | Pyranose 2-oxidase (EC 1.1.3.10) | protein | 573 | 25% helix, 23% strand | Q7ZA32 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- SHG · 2-deoxy-2-fluoro-beta-D-glucopyranose · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 8 copies · chains A, B, D, C, E, F, H, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 636 | 0.87 | 0.92 | 70 | FAD, SHG |
| 2 | 676 | 0.87 | 0.91 | 69 | FAD, SHG |
| 3 | 701 | 0.87 | 0.90 | 76 | FAD, SHG |
| 4 | 623 | 0.87 | 0.91 | 68 | FAD, SHG |
| 5 | 704 | 0.87 | 0.90 | 76 | FAD, SHG |
Interfaces
12 interfaces between chains.
- A–B · 2861 Ų buried · 48 hydrogen bonds · protein-protein
- G–H · 2846 Ų buried · 46 hydrogen bonds · protein-protein
- E–F · 2820 Ų buried · 46 hydrogen bonds · protein-protein
- C–D · 2790 Ų buried · 41 hydrogen bonds · protein-protein
- B–C · 1215 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor (flavinylation).
Compared structures
- 3K4M · Pyranose 2-oxidase Y456W mutant in complex with 2FG · 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 Q7ZA32
- Elsewhere: RCSB PDB 3K4M · PDBe 3K4M · UniProt Q7ZA32
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.