MolNFT v1 · #99930 · protein
Pyranose 2-oxidase from phanerochaete chrysosporium, wild type from natural source
4MIF: “Pyranose 2-oxidase from phanerochaete chrysosporium, wild type from natural source”. X-ray diffraction, 2 ligands (FDA, MG), 20 pockets (best druggability 0.89). MolNFT v1 #99930 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4MIF
- Type
- protein
- Length
- 2,297 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyranose 2-oxidase
- EC
- 1.1.3.10
- UniProt
- Q6QWR1
- Ligands
- FDA, MG
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Pyranose 2-oxidase (EC 1.1.3.10) | protein | 572 | 29% helix, 22% strand | Q6QWR1 |
| B | Pyranose 2-oxidase (EC 1.1.3.10) | protein | 581 | 29% helix, 22% strand | Q6QWR1 |
Ligands and binding sites
- FDA · Dihydroflavine-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 792 | 0.89 | 0.92 | 104 | FDA |
| 2 | 429 | 0.87 | 0.94 | 67 | FDA |
| 3 | 464 | 0.87 | 0.94 | 73 | FDA |
| 4 | 497 | 0.86 | 0.93 | 76 | FDA |
| 5 | 280 | 0.80 | 0.92 | 46 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3449 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 3316 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 1110 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 1106 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 591 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 4MIF · Pyranose 2-oxidase from Phanerochaete chrysosporium, wild type from natural source · the same entry in another collection · chain A against A, TM-score 1.00
- Q6QWR1 · AlphaFold monomer V2.0 prediction for pyranose 2-oxidase (Q6QWR1) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 4MIF · PDBe 4MIF · UniProt Q6QWR1
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