Research workbench
Class II fructose-1,6-bisphosphate aldolase E149A variant of helicobacter pylori with cleavage products
Analyse Class II fructose-1,6-bisphosphate aldolase E149A 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
- 5UD0
- Type
- protein
- Length
- 573 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, G3H, ZN, NA, CA
- Pockets
- 3 · best druggability 0.45
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fructose-bisphosphate aldolase (EC 4.1.2.13) | protein | 282 | 55% helix, 15% strand | P56109 |
| B | Fructose-bisphosphate aldolase (EC 4.1.2.13) | protein | 291 | 53% helix, 15% strand | P56109 |
Ligands and binding sites
- 13P · 1,3-dihydroxyacetonephosphate · ligand · chains B
- G3H · Glyceraldehyde-3-phosphate · ligand · chains A, B
- ZN · Zinc ion · metal · 3 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 107 | 0.45 | 0.79 | 26 | ZN, 13P, G3H |
| 2 | 144 | 0.43 | 0.76 | 26 | empty |
| 3 | 55 | 0.31 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1943 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 5UD0 · Class II fructose-1,6-bisphosphate aldolase E149A variant of Helicobacter pylori with… · 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 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 5UD0 · PDBe 5UD0 · UniProt P56109
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