Research workbench
Crystal structure of recombinant pyranose 2-oxidase H548N mutant
Analyse Crystal structure of recombinant pyranose 2-oxidase H548N mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IGM
- 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
- 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, G, H | Pyranose oxidase (EC 1.1.3.10) | protein | 577 | 25% helix, 24% strand | Q7ZA32 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 8 copies · chains A, B, D, C, 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 | 740 | 0.87 | 0.90 | 78 | FAD |
| 2 | 725 | 0.87 | 0.90 | 76 | FAD |
| 3 | 718 | 0.87 | 0.90 | 70 | FAD |
| 4 | 760 | 0.87 | 0.90 | 77 | FAD |
| 5 | 702 | 0.87 | 0.90 | 74 | FAD |
Interfaces
12 interfaces between chains.
- G–H · 2861 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 2840 Ų buried · 44 hydrogen bonds · protein-protein
- E–F · 2819 Ų buried · 43 hydrogen bonds · protein-protein
- D–C · 2795 Ų buried · 41 hydrogen bonds · protein-protein
- B–C · 1118 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor (flavinylation).
Compared structures
- 2IGM · Crystal structure of recombinant pyranose 2-oxidase H548N mutant · the same entry in another collection · chain G against G, 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 2IGM · PDBe 2IGM · UniProt Q7ZA32
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