Research workbench
Structure of E.COLI fructose 1,6-bisphosphate aldolase, acetate bound form
Analyse Structure of E.COLI fructose 1,6-bisphosphate aldolase, acetate bound form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GK8
- Type
- protein
- Length
- 663 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fructose-bisphosphate aldolase class 2
- EC
- 4.1.2.13
- UniProt
- P0AB71
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fructose-bisphosphate aldolase class 2 (EC 4.1.2.13) | protein | 332 | 53% helix, 15% strand | P0AB71 |
| B | Fructose-bisphosphate aldolase class 2 (EC 4.1.2.13) | protein | 331 | 53% helix, 15% strand | P0AB71 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 334 | 0.74 | 0.86 | 64 | ACT, ZN |
| 2 | 126 | 0.39 | 0.74 | 18 | ACT, ZN |
| 3 | 113 | 0.38 | 0.74 | 13 | GOL |
| 4 | 73 | 0.37 | 0.77 | 14 | GOL |
| 5 | 82 | 0.35 | 0.75 | 13 | GOL |
Interfaces
1 interface between chains.
- A–B · 2477 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 5GK8 · Structure of E.Coli fructose 1,6-bisphosphate aldolase, Acetate bound form · the same entry in another collection · chain A against A, TM-score 1.00
- P0AB71 · AlphaFold monomer V2.0 prediction for fructose-bisphosphate aldolase class 2 (P0AB71) · 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 P0AB71
- Elsewhere: RCSB PDB 5GK8 · PDBe 5GK8 · UniProt P0AB71
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