Research workbench
Pyranose 2-oxidase H167A mutant with flavin N(5) sulfite adduct
Analyse Pyranose 2-oxidase H167A mutant with flavin N(5) sulfite adduct in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LSM
- Type
- protein
- Length
- 1,150 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyranose 2-oxidase
- EC
- 1.1.3.10
- UniProt
- Q7ZA32
- Ligands
- SFD, GLC, SO3
- Pockets
- 13 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyranose 2-oxidase (EC 1.1.3.10) | protein | 574 | 25% helix, 24% strand | Q7ZA32 |
| B | Pyranose 2-oxidase (EC 1.1.3.10) | protein | 576 | 24% helix, 24% strand | Q7ZA32 |
Ligands and binding sites
- SFD · (S)-10-((2S,3S,4R)-5-((S)-((S)-(((2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxy-tetrahydrofuran-2-yl)methoxy)(hydroxy)phosphoryloxy)(hydroxy)phosphoryloxy)-2,3,4-trihydroxypentyl)-7,8-dimethyl-2,4-dioxo-2,3,4,4A-tetrahydrobenzo[g]pteridine-5(10H)-sulfonic acid · ligand · 2 copies · chains A, B
- GLC · alpha-D-glucopyranose · sugar · chains A
- SO3 · Sulfite ion · ion · 4 copies · chains A, B
- 12P · Dodecaethylene glycol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 499 | 0.88 | 0.95 | 65 | SFD |
| 2 | 505 | 0.88 | 0.94 | 65 | SFD |
| 3 | 1051 | 0.79 | 0.81 | 91 | empty |
| 4 | 714 | 0.79 | 0.83 | 71 | empty |
| 5 | 316 | 0.72 | 0.85 | 54 | empty |
Interfaces
1 interface between chains.
- A–B · 2726 Ų buried · 41 hydrogen bonds · protein-protein
Compared structures
- 3LSM · Pyranose 2-oxidase H167A mutant with flavin N(5) sulfite adduct · 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 3LSM · PDBe 3LSM · UniProt Q7ZA32
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