MolNFT v1 · #119935 · protein
Native structure of fructose 1,6-bisphosphate aldolase from escherichia COLI at 1.8 ångström resolution
5GK3 · Fructose-bisphosphate aldolase class 2: “Native structure of fructose 1,6-bisphosphate aldolase from escherichia COLI at 1.8 ångström resolution”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best druggability 0.77). MolNFT v1…
- PDB
- 5GK3
- Type
- protein
- Length
- 666 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 0.77
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fructose-bisphosphate aldolase class 2 (EC 4.1.2.13) | protein | 334 | 53% helix, 14% strand | P0AB71 |
| B | Fructose-bisphosphate aldolase class 2 (EC 4.1.2.13) | protein | 332 | 53% helix, 14% strand | P0AB71 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 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 | 385 | 0.77 | 0.87 | 74 | empty |
| 2 | 77 | 0.38 | 0.77 | 13 | GOL |
| 3 | 78 | 0.37 | 0.77 | 15 | empty |
| 4 | 73 | 0.36 | 0.77 | 16 | GOL |
| 5 | 106 | 0.34 | 0.72 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 2440 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 5GK3 · Native structure of fructose 1,6-bisphosphate aldolase from Escherichia coli at 1.8… · 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 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 P0AB71
- Elsewhere: RCSB PDB 5GK3 · PDBe 5GK3 · UniProt P0AB71
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