MolNFT v1 · #102276 · protein
Crystal structure of a putative alpha-GALACTOSIDASE/MELIBIASE (BF4189) from bacteroides fragilis nctc 9343 at 2.00 a resolution
4OGZ: “Crystal structure of a putative alpha-GALACTOSIDASE/MELIBIASE (BF4189) from bacteroides fragilis nctc 9343 at…”. X-ray diffraction, 1 ligand (PO4), 7 pockets (best druggability 0.80). MolNFT v1 #102276 on GenesisL1: 3D structure…
- PDB
- 4OGZ
- Type
- protein
- Length
- 927 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative alpha-GALACTOSIDASE/MELIBIASE
- EC
- 3.2.1.22
- UniProt
- Q5L7T7
- Ligands
- PO4
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative alpha-GALACTOSIDASE/MELIBIASE (EC 3.2.1.22) | protein | 461 | 23% helix, 28% strand | Q5L7T7 |
| B | Putative alpha-GALACTOSIDASE/MELIBIASE (EC 3.2.1.22) | protein | 466 | 24% helix, 28% strand | Q5L7T7 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · chains B
- PEG · Di(hydroxyethyl)ether · additive · 8 copies · chains A, B
- PGE · Triethylene glycol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 209 | 0.80 | 0.94 | 38 | PEG |
| 2 | 217 | 0.78 | 0.92 | 42 | PGE |
| 3 | 958 | 0.71 | 0.75 | 69 | PEG |
| 4 | 129 | 0.39 | 0.74 | 20 | PEG |
| 5 | 135 | 0.38 | 0.73 | 25 | PEG |
Interfaces
1 interface between chains.
- A–B · 481 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified, 2 disulfide (engineered, disulfide).
Compared structures
- 4OGZ · Crystal structure of a putative alpha-galactosidase/melibiase (BF4189) from Bacteroides… · 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 Q5L7T7
- Elsewhere: RCSB PDB 4OGZ · PDBe 4OGZ · UniProt Q5L7T7
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