MolNFT v1 · #63595 · protein
Crystal structure of putative glucosidase lpld from bacillus subtilis
3FEF · Putative glucosidase lpld, alpha-galacturonidase: “Crystal structure of putative glucosidase lpld from bacillus subtilis”. X-ray diffraction, 2 ligands (MG, SO4), 20 pockets (best druggability 0.79). MolNFT v1 #63595 on GenesisL1…
- PDB
- 3FEF
- Type
- protein
- Length
- 1,736 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative glucosidase lpld, alpha-galacturonidase
- EC
- 3.2.1.67
- UniProt
- P39130
- Ligands
- MG, SO4
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Putative glucosidase lpld, alpha-galacturonidase (EC 3.2.1.67) | protein | 434 | 46% helix, 17% strand | P39130 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 7 copies · chains A, C, B, 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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 988 | 0.79 | 0.80 | 81 | SO4, MG |
| 2 | 1024 | 0.78 | 0.80 | 82 | SO4, MG |
| 3 | 1053 | 0.78 | 0.80 | 78 | SO4, MG |
| 4 | 1054 | 0.77 | 0.79 | 81 | SO4, MG |
| 5 | 201 | 0.66 | 0.85 | 42 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1212 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1206 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1047 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 1022 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified (engineered).
Compared structures
- 3FEF · Crystal structure of putative glucosidase lplD from bacillus subtilis · the same entry in another collection · chain A against A, TM-score 1.00
- P39130 · AlphaFold monomer V2.0 prediction for alpha-galacturonidase (P39130) · a predicted model of the same protein · 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 P39130
- Elsewhere: RCSB PDB 3FEF · PDBe 3FEF · UniProt P39130
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