MolNFT v1 · #156442 · protein
Crystal structure of the E496A mutant of hsbgla
6M4F · Beta-galactosidase-like enzyme: “Crystal structure of the E496A mutant of hsbgla”. X-ray diffraction, 2 ligands (NAG, MAN), 13 pockets (best druggability 0.75). MolNFT v1 #156442 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6M4F
- Type
- protein
- Length
- 2,171 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-galactosidase-like enzyme
- UniProt
- Q564N5
- Ligands
- NAG, MAN
- Pockets
- 13 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Beta-galactosidase-like enzyme | protein | 542 | 45% helix, 12% strand | Q564N5 |
| C | Beta-galactosidase-like enzyme | protein | 543 | 45% helix, 12% strand | Q564N5 |
| G | Beta-galactosidase-like enzyme | protein | 544 | 45% helix, 11% strand | Q564N5 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 24 copies · chains A, C, E, G
- MAN · alpha-D-mannopyranose · sugar · 5 copies · chains C, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 446 | 0.75 | 0.84 | 53 | empty |
| 2 | 77 | 0.75 | 0.98 | 31 | empty |
| 3 | 68 | 0.72 | 0.98 | 31 | empty |
| 4 | 564 | 0.68 | 0.78 | 60 | empty |
| 5 | 564 | 0.68 | 0.78 | 61 | empty |
Interfaces
3 interfaces between chains.
- E–G · 1621 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1605 Ų buried · 18 hydrogen bonds · protein-protein
- C–E · 210 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 21 glycan, 12 disulfide (N-glycosylation, disulfide, O-glycosylation).
Compared structures
- 6M4F · Crystal structure of the E496A mutant of HsBglA · 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 Q564N5
- Elsewhere: RCSB PDB 6M4F · PDBe 6M4F · UniProt Q564N5
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