MolNFT v1 · #40127 · protein
Crystal structure of pyranose 2-oxidase H167A mutant with 2-fluoro-2- deoxy-D-glucose
2IGO · Pyranose oxidase: “Crystal structure of pyranose 2-oxidase H167A mutant with 2-fluoro-2- deoxy-D-glucose”. X-ray diffraction, 2 ligands (SHG, FAD), 20 pockets (best druggability 0.87). MolNFT v1 #40127 on GenesisL1: 3D structure…
- PDB
- 2IGO
- Type
- protein
- Length
- 4,616 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyranose oxidase
- EC
- 1.1.3.10
- UniProt
- Q7ZA32
- Ligands
- SHG, FAD
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, C, E, F, H, G | Pyranose oxidase (EC 1.1.3.10) | protein | 577 | 25% helix, 24% strand | Q7ZA32 |
Ligands and binding sites
- SHG · 2-deoxy-2-fluoro-beta-D-glucopyranose · ligand · 8 copies · chains A, B, D, C, E, F, H, G
- FAD · Flavin-adenine dinucleotide · ligand · 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 | 697 | 0.87 | 0.91 | 70 | SHG, FAD |
| 2 | 769 | 0.87 | 0.90 | 78 | SHG, FAD |
| 3 | 730 | 0.87 | 0.90 | 76 | SHG, FAD |
| 4 | 729 | 0.87 | 0.90 | 76 | SHG, FAD |
| 5 | 713 | 0.86 | 0.90 | 73 | SHG, FAD |
Interfaces
12 interfaces between chains.
- A–B · 2838 Ų buried · 46 hydrogen bonds · protein-protein
- H–G · 2827 Ų buried · 44 hydrogen bonds · protein-protein
- E–F · 2800 Ų buried · 47 hydrogen bonds · protein-protein
- D–C · 2781 Ų buried · 43 hydrogen bonds · protein-protein
- B–C · 1173 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 2IGO · Crystal structure of pyranose 2-oxidase H167A mutant with 2-fluoro-2-deoxy-D-glucose · 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 2IGO · PDBe 2IGO · UniProt Q7ZA32
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