Research workbench
Archaeal fructose 1,6-bisphosphate aldolase covalently bound to the substrate dihydroxyacetone phosphate
Analyse Archaeal fructose 1,6-bisphosphate aldolase covalently bound to the substrate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1OK4
- Type
- protein
- Length
- 2,502 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fructose-bisphosphate aldolase class I
- EC
- 4.1.2.13
- UniProt
- P58315
- Ligands
- 13P
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, F, G, H, I, J | Fructose-bisphosphate aldolase class I (EC 4.1.2.13) | protein | 250 | 46% helix, 16% strand | P58315 |
| E | Fructose-bisphosphate aldolase class I (EC 4.1.2.13) | protein | 252 | 46% helix, 16% strand | P58315 |
Ligands and binding sites
- 13P · 1,3-dihydroxyacetonephosphate · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1041 | 0.73 | 0.76 | 77 | empty |
| 2 | 754 | 0.73 | 0.79 | 68 | empty |
| 3 | 488 | 0.71 | 0.81 | 53 | empty |
| 4 | 491 | 0.66 | 0.78 | 33 | empty |
| 5 | 215 | 0.62 | 0.82 | 34 | empty |
Interfaces
15 interfaces between chains.
- I–J · 1554 Ų buried · 23 hydrogen bonds · protein-protein
- D–E · 1547 Ų buried · 23 hydrogen bonds · protein-protein
- H–I · 1545 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1545 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1545 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 covalent (covalent ligand).
Compared structures
- 1OK4 · Archaeal fructose 1,6-bisphosphate aldolase covalently bound to the substrate… · the same entry in another collection · chain J against J, TM-score 1.00
- P58315 · AlphaFold monomer V2.0 prediction for fructose-bisphosphate aldolase class 1 (P58315) · 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 P58315
- Elsewhere: RCSB PDB 1OK4 · PDBe 1OK4 · UniProt P58315
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