Research workbench
Crystal structure of pyranose 2-oxidase
Analyse Crystal structure of pyranose 2-oxidase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TT0
- Type
- protein
- Length
- 2,302 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyranose oxidase
- EC
- 1.1.3.10
- Ligands
- FAD
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pyranose oxidase (EC 1.1.3.10) | protein | 577 | 24% helix, 24% strand | — |
| C, D | Pyranose oxidase (EC 1.1.3.10) | protein | 574 | 24% helix, 23% strand | — |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- 12P · Dodecaethylene glycol · additive · 20 copies · chains A, D, B, C
- ACT · Acetate ion · additive · 4 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 496 | 0.88 | 0.95 | 63 | ACT, FAD |
| 2 | 495 | 0.88 | 0.95 | 63 | ACT, FAD |
| 3 | 491 | 0.88 | 0.94 | 63 | ACT, FAD |
| 4 | 495 | 0.87 | 0.94 | 62 | ACT, FAD |
| 5 | 1034 | 0.84 | 0.85 | 120 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2809 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 2804 Ų buried · 41 hydrogen bonds · protein-protein
- A–D · 1196 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 1186 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 472 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (flavinylation).
Compared structures
- 1TT0 · Crystal Structure of Pyranose 2-Oxidase · 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
- Elsewhere: RCSB PDB 1TT0 · PDBe 1TT0
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