Research workbench
Class II fructose-1,6-bisphosphate aldolase from helicobacter pylori in complex with N-(4-hydroxybutyl)- glycolohydroxamic acid bis- phosphate, a competitive inhibitor
Analyse Class II fructose-1,6-bisphosphate aldolase from helicobacter pylori in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3N9S
- Type
- protein
- Length
- 602 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
- D0IR47
- Ligands
- TD4, ZN, CA, NA
- Pockets
- 2 · best druggability 0.47
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fructose-bisphosphate aldolase (EC 4.1.2.13) | protein | 307 | 50% helix, 15% strand | D0IR47 |
| B | Fructose-bisphosphate aldolase (EC 4.1.2.13) | protein | 295 | 52% helix, 15% strand | D0IR47 |
Ligands and binding sites
- TD4 · 4-{hydroxy[(phosphonooxy)acetyl]amino}butyl dihydrogen phosphate · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 101 | 0.47 | 0.81 | 28 | TD4 |
| 2 | 109 | 0.46 | 0.80 | 23 | TD4, ZN |
Interfaces
1 interface between chains.
- A–B · 1923 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 3N9S · Class II fructose-1,6-bisphosphate aldolase from helicobacter pylori in complex with… · the same entry in another collection · 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 D0IR47
- Elsewhere: RCSB PDB 3N9S · PDBe 3N9S · UniProt D0IR47
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