MolNFT v1 · #139061 · protein
KFLA1895 D451A mutant in complex with cyclobis-(1->6)-alpha-nigerosyl
5X3J · Glycoside hydrolase family 31: “KFLA1895 D451A mutant in complex with cyclobis-(1->6)-alpha-nigerosyl”. X-ray diffraction, 2 ligands (GLC, SO4), 8 pockets (best druggability 0.77). MolNFT v1 #139061 on GenesisL1: 3D structure…
- PDB
- 5X3J
- Type
- protein
- Length
- 1,432 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoside hydrolase family 31
- UniProt
- D2PPM7
- Ligands
- GLC, SO4
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycoside hydrolase family 31 | protein | 718 | 26% helix, 26% strand | D2PPM7 |
| B | Glycoside hydrolase family 31 | protein | 714 | 26% helix, 26% strand | D2PPM7 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 8 copies · chains A, B
- SO4 · Sulfate ion · ion · 20 copies · chains A, B
- GOL · Glycerol · additive · 6 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 879 | 0.77 | 0.80 | 107 | SO4 |
| 2 | 811 | 0.72 | 0.78 | 75 | SO4 |
| 3 | 590 | 0.72 | 0.80 | 48 | SO4 |
| 4 | 461 | 0.67 | 0.79 | 62 | GLC |
| 5 | 241 | 0.60 | 0.80 | 28 | GLC |
Interfaces
1 interface between chains.
- A–B · 873 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5X3J · Kfla1895 D451A mutant in complex with cyclobis-(1->6)-alpha-nigerosyl · the same entry in another collection · chain A against A, TM-score 1.00
- D2PPM7 · AlphaFold monomer V2.0 prediction for 1,3-alpha-isomaltosidase (D2PPM7) · a predicted model of the same protein · chain B 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 D2PPM7
- Elsewhere: RCSB PDB 5X3J · PDBe 5X3J · UniProt D2PPM7
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