Research workbench
Class II fructose-1,6-bisphosphate aldolase of escherichia COLI with dhap
Analyse Class II fructose-1,6-bisphosphate aldolase of escherichia COLI with dhap in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VJD
- Type
- protein
- Length
- 686 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
- 13P, NA, ZN
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fructose-bisphosphate aldolase class 2 (EC 4.1.2.13) | protein | 343 | 51% helix, 15% strand | P0AB71 |
| B | Fructose-bisphosphate aldolase class 2 (EC 4.1.2.13) | protein | 343 | 51% helix, 15% strand | P0AB71 |
Ligands and binding sites
- 13P · 1,3-dihydroxyacetonephosphate · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 4 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 72 | 0.73 | 0.98 | 25 | empty |
| 2 | 69 | 0.72 | 0.97 | 26 | empty |
| 3 | 209 | 0.51 | 0.77 | 38 | 13P |
| 4 | 95 | 0.41 | 0.78 | 22 | 13P |
| 5 | 61 | 0.38 | 0.80 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 2721 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 5VJD · Class II fructose-1,6-bisphosphate aldolase of Escherichia coli with DHAP · 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 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 P0AB71
- Elsewhere: RCSB PDB 5VJD · PDBe 5VJD · UniProt P0AB71
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