Research workbench
Structure of human aldolase B associated with hereditary fructose intolerance (A149P), at 291K
Analyse Structure of human aldolase B associated with hereditary fructose intolerance… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XDM
- Type
- protein
- Length
- 2,400 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fructose-bisphosphate aldolase B
- EC
- 4.1.2.13
- UniProt
- P05062
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 7 distinct chains · 53% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fructose-bisphosphate aldolase B (EC 4.1.2.13) | protein | 303 | 50% helix, 11% strand | P05062 |
| B, Y | Fructose-bisphosphate aldolase B (EC 4.1.2.13) | protein | 304 | 55% helix, 13% strand | P05062 |
| C | Fructose-bisphosphate aldolase B (EC 4.1.2.13) | protein | 299 | 53% helix, 11% strand | P05062 |
| D | Fructose-bisphosphate aldolase B (EC 4.1.2.13) | protein | 296 | 54% helix, 12% strand | P05062 |
| W | Fructose-bisphosphate aldolase B (EC 4.1.2.13) | protein | 297 | 54% helix, 11% strand | P05062 |
| X | Fructose-bisphosphate aldolase B (EC 4.1.2.13) | protein | 302 | 53% helix, 10% strand | P05062 |
| Z | Fructose-bisphosphate aldolase B (EC 4.1.2.13) | protein | 295 | 52% helix, 11% strand | P05062 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D, W, X, Y, Z
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 901 | 0.81 | 0.83 | 62 | empty |
| 2 | 922 | 0.81 | 0.83 | 65 | empty |
| 3 | 50 | 0.69 | 0.97 | 15 | empty |
| 4 | 304 | 0.66 | 0.82 | 55 | SO4 |
| 5 | 262 | 0.65 | 0.82 | 40 | SO4 |
Interfaces
13 interfaces between chains.
- C–D · 861 Ų buried · 10 hydrogen bonds · protein-protein
- W–X · 861 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 858 Ų buried · 10 hydrogen bonds · protein-protein
- Y–Z · 855 Ų buried · 10 hydrogen bonds · protein-protein
- B–Y · 360 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1XDM · Structure of human aldolase B associated with hereditary fructose intolerance (A149P), at… · the same entry in another collection · chain Z against Z, TM-score 1.00
- P05062 · AlphaFold monomer V2.0 prediction for fructose-bisphosphate aldolase B (P05062) · a predicted model of the same protein · chain X against A, TM-score 0.99
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 P05062
- Elsewhere: RCSB PDB 1XDM · PDBe 1XDM · UniProt P05062
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