Research workbench
Apo structure of fructose 1,6-bisphosphate aldolase from escherichia COLI at 1.9 ångström resolution
Analyse Apo structure of fructose 1,6-bisphosphate aldolase from escherichia COLI at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GK5
- Type
- protein
- Length
- 2,661 residues
- Chains
- 8
- 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
- 20 · best druggability 0.80
Structure
x-ray diffraction · 5 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, 14% strand | P0AB71 |
| B, D, H | Fructose-bisphosphate aldolase class 2 (EC 4.1.2.13) | protein | 331 | 53% helix, 15% strand | P0AB71 |
| C, G | Fructose-bisphosphate aldolase class 2 (EC 4.1.2.13) | protein | 335 | 53% helix, 14% strand | P0AB71 |
| E | Fructose-bisphosphate aldolase class 2 (EC 4.1.2.13) | protein | 334 | 53% helix, 14% strand | P0AB71 |
| F | Fructose-bisphosphate aldolase class 2 (EC 4.1.2.13) | protein | 332 | 53% helix, 15% strand | P0AB71 |
Ligands and binding sites
- ZN · Zinc ion · metal · 14 copies · chains A, B, C, D, E, F, G, H
- GOL · Glycerol · additive · 7 copies · chains A, B, G, C, D, E, H
- PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains A, B, C, D, E, F, G, H
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 | 154 | 0.80 | 0.96 | 46 | empty |
| 2 | 980 | 0.79 | 0.81 | 99 | GOL |
| 3 | 327 | 0.74 | 0.86 | 65 | empty |
| 4 | 74 | 0.72 | 0.97 | 25 | PEG |
| 5 | 665 | 0.70 | 0.78 | 56 | empty |
Interfaces
9 interfaces between chains.
- E–F · 2453 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 2423 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 2411 Ų buried · 19 hydrogen bonds · protein-protein
- G–H · 2411 Ų buried · 20 hydrogen bonds · protein-protein
- B–G · 364 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5GK5 · Apo structure of fructose 1,6-bisphosphate aldolase from Escherichia coli at 1.9 angstrom… · the same entry in another collection · chain H against H, 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 H 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 5GK5 · PDBe 5GK5 · UniProt P0AB71
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