Research workbench
Class II fructose-1,6-bisphosphate aldolase H180Q variant of helicobacter pylori with dhap
Analyse Class II fructose-1,6-bisphosphate aldolase H180Q variant of helicobacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UD2
- Type
- protein
- Length
- 584 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fructose-bisphosphate aldolase
- EC
- 4.1.2.13
- UniProt
- P56109
- Ligands
- 13P, ZN, NA
- Pockets
- 2 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Fructose-bisphosphate aldolase (EC 4.1.2.13) | protein | 292 | 53% helix, 15% strand | P56109 |
Ligands and binding sites
- 13P · 1,3-dihydroxyacetonephosphate · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 278 | 0.59 | 0.78 | 50 | ZN, 13P |
| 2 | 257 | 0.57 | 0.78 | 42 | ZN, 13P |
Interfaces
1 interface between chains.
- A–B · 1956 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 5UD2 · Class II fructose-1,6-bisphosphate aldolase H180Q variant of Helicobacter pylori with DHAP · the same entry in another collection · chain A against A, TM-score 1.00
- P56109 · AlphaFold monomer V2.0 prediction for fructose-bisphosphate aldolase (P56109) · 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 P56109
- Elsewhere: RCSB PDB 5UD2 · PDBe 5UD2 · UniProt P56109
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