MolNFT v1 · #99931 · protein
Pyranose 2-oxidase from phanerochaete chrysosporium, recombinant wild type
4MIG: “Pyranose 2-oxidase from phanerochaete chrysosporium, recombinant wild type”. X-ray diffraction, 3 ligands (FDA, G3F, MN), 20 pockets (best druggability 0.89). MolNFT v1 #99931 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4MIG
- Type
- protein
- Length
- 2,293 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, G3F, MN
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Pyranose 2-oxidase (EC 1.1.3.10) | protein | 570 | 29% helix, 22% strand | Q6QWR1 |
| B | Pyranose 2-oxidase (EC 1.1.3.10) | protein | 574 | 29% helix, 23% strand | Q6QWR1 |
| C | Pyranose 2-oxidase (EC 1.1.3.10) | protein | 579 | 29% helix, 22% strand | Q6QWR1 |
Ligands and binding sites
- FDA · Dihydroflavine-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- G3F · 3-deoxy-3-fluoro-beta-D-glucopyranose · ligand · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1018 | 0.89 | 0.91 | 129 | FDA, G3F |
| 2 | 1097 | 0.89 | 0.91 | 132 | FDA, G3F |
| 3 | 1111 | 0.89 | 0.90 | 124 | FDA, G3F |
| 4 | 1119 | 0.88 | 0.89 | 120 | FDA, G3F |
| 5 | 495 | 0.80 | 0.87 | 73 | empty |
Interfaces
6 interfaces between chains.
- C–D · 3318 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 3174 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 1098 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1092 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 604 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 4MIG · Pyranose 2-oxidase from Phanerochaete chrysosporium, recombinant wild type · the same entry in another collection · chain B against B, 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 0.99
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 4MIG · PDBe 4MIG · UniProt Q6QWR1
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