MolNFT v1 · #100139 · protein
Pyranose 2-oxidase H167A mutant with 2-fluorinated galactose
4MOL: “Pyranose 2-oxidase H167A mutant with 2-fluorinated galactose”. X-ray diffraction, 2 ligands (FAD, 2FG), 20 pockets (best druggability 0.88). MolNFT v1 #100139 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4MOL
- Type
- protein
- Length
- 2,295 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
- Q7ZA32
- Ligands
- FAD, 2FG
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Pyranose 2-oxidase (EC 1.1.3.10) | protein | 573 | 25% helix, 23% strand | Q7ZA32 |
| B | Pyranose 2-oxidase (EC 1.1.3.10) | protein | 576 | 24% helix, 24% strand | Q7ZA32 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- 2FG · 2-deoxy-2-fluoro-beta-D-galactopyranose · ligand · 4 copies · chains A, B, C, D
- 12P · Dodecaethylene glycol · additive · 4 copies · chains A, D, B, C
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 522 | 0.88 | 0.95 | 67 | FAD, 2FG |
| 2 | 520 | 0.88 | 0.94 | 65 | FAD, 2FG |
| 3 | 509 | 0.88 | 0.95 | 64 | FAD, 2FG |
| 4 | 513 | 0.87 | 0.94 | 62 | FAD, 2FG |
| 5 | 1006 | 0.82 | 0.83 | 100 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2693 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 2668 Ų buried · 46 hydrogen bonds · protein-protein
- B–C · 1171 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 1170 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 473 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4MOL · Pyranose 2-oxidase H167A mutant with 2-fluorinated galactose · 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 4MOL · PDBe 4MOL · UniProt Q7ZA32
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