MolNFT v1 · #135910 · protein
Class II fructose-1,6-bisphosphate aldolase H180Q variant of helicobacter pylori with tbp
5UD4 · Fructose-bisphosphate aldolase: “Class II fructose-1,6-bisphosphate aldolase H180Q variant of helicobacter pylori with tbp”. X-ray diffraction, 3 ligands (P6T, ZN, NA), 2 pockets (best druggability 0.60). MolNFT v1 #135910 on…
- PDB
- 5UD4
- Type
- protein
- Length
- 586 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
- P6T, ZN, NA
- Pockets
- 2 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Fructose-bisphosphate aldolase (EC 4.1.2.13) | protein | 293 | 52% helix, 15% strand | P56109 |
Ligands and binding sites
- P6T · 1,6-di-O-phosphono-D-tagatose · 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 | 234 | 0.60 | 0.81 | 42 | ZN, P6T |
| 2 | 204 | 0.57 | 0.80 | 37 | ZN, P6T |
Interfaces
1 interface between chains.
- A–B · 1957 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 5UD4 · Class II fructose-1,6-bisphosphate aldolase H180Q variant of Helicobacter pylori with TBP · 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 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 P56109
- Elsewhere: RCSB PDB 5UD4 · PDBe 5UD4 · UniProt P56109
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