Research workbench
Pyranose 2-oxidase from phanerochaete chrysosporium, recombinant H158A mutant
Analyse Pyranose 2-oxidase from phanerochaete chrysosporium, recombinant H158A mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MIH
- Type
- protein
- Length
- 4,620 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
- Q6QWR1
- Ligands
- FAD, G3F
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Pyranose 2-oxidase (EC 1.1.3.10) | protein | 576 | 28% helix, 22% strand | Q6QWR1 |
| B, C, D, F, G, H | Pyranose 2-oxidase (EC 1.1.3.10) | protein | 578 | 27% helix, 22% strand | Q6QWR1 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- G3F · 3-deoxy-3-fluoro-beta-D-glucopyranose · ligand · 8 copies · chains A, B, C, D, E, F, G, 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1185 | 0.89 | 0.91 | 133 | FAD, G3F |
| 2 | 1131 | 0.89 | 0.90 | 127 | FAD, G3F |
| 3 | 1116 | 0.89 | 0.90 | 133 | FAD, G3F |
| 4 | 1152 | 0.89 | 0.90 | 135 | FAD, G3F |
| 5 | 1183 | 0.88 | 0.90 | 132 | FAD, G3F |
Interfaces
13 interfaces between chains.
- C–D · 3259 Ų buried · 35 hydrogen bonds · protein-protein
- E–F · 3139 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 3085 Ų buried · 20 hydrogen bonds · protein-protein
- G–H · 3065 Ų buried · 26 hydrogen bonds · protein-protein
- E–H · 1084 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4MIH · Pyranose 2-oxidase from Phanerochaete chrysosporium, recombinant H158A mutant · the same entry in another collection · chain H against H, TM-score 1.00
- Q6QWR1 · AlphaFold monomer V2.0 prediction for pyranose 2-oxidase (Q6QWR1) · a predicted model of the same protein · chain B 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 Q6QWR1
- Elsewhere: RCSB PDB 4MIH · PDBe 4MIH · UniProt Q6QWR1
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