MolNFT v1 · #146886 · protein
2.25 ångström resolution crystal structure of 6-phospho-alpha- glucosidase from klebsiella pneumoniae in complex with NAD and MN2+.
6DVV · 6-phospho-alpha-glucosidase: “2.25 ångström resolution crystal structure of 6-phospho-alpha- glucosidase from klebsiella pneumoniae in…”. X-ray diffraction, 4 ligands (NAD, MN, SO4), 7 pockets (best druggability 0.81). MolNFT v1…
- PDB
- 6DVV
- Type
- protein
- Length
- 866 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6-phospho-alpha-glucosidase
- EC
- 3.2.1.122
- UniProt
- Q9AGA6
- Ligands
- NAD, MN, SO4, CL
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 6-phospho-alpha-glucosidase (EC 3.2.1.122) | protein | 435 | 51% helix, 17% strand | Q9AGA6 |
| B | 6-phospho-alpha-glucosidase (EC 3.2.1.122) | protein | 431 | 50% helix, 17% strand | Q9AGA6 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · chains A
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 10 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 955 | 0.81 | 0.83 | 89 | NAD, SO4 |
| 2 | 878 | 0.76 | 0.80 | 85 | SO4, PEG |
| 3 | 284 | 0.64 | 0.81 | 38 | empty |
| 4 | 393 | 0.63 | 0.78 | 41 | SO4 |
| 5 | 333 | 0.60 | 0.78 | 47 | SO4 |
Interfaces
1 interface between chains.
- A–B · 964 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified (engineered).
Compared structures
- 6DVV · 2.25 Angstrom Resolution Crystal Structure of 6-phospho-alpha-glucosidase from Klebsiella… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9AGA6 · AlphaFold monomer V2.0 prediction for 6-phospho-alpha-glucosidase (Q9AGA6) · 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 Q9AGA6
- Elsewhere: RCSB PDB 6DVV · PDBe 6DVV · UniProt Q9AGA6
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