Research workbench
Aquifex aeolicus KDO8PS in complex with pep, A5P, ZN2+
Analyse Aquifex aeolicus KDO8PS in complex with pep, A5P, ZN2+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2A2I
- Type
- protein
- Length
- 518 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-dehydro-3-deoxyphosphooctonate aldolase
- EC
- 2.5.1.55
- UniProt
- O66496
- Ligands
- PEP, A5P, ZN
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55) | protein | 263 | 41% helix, 21% strand | O66496 |
| B | 2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55) | protein | 255 | 44% helix, 20% strand | O66496 |
Ligands and binding sites
- PEP · Phosphoenolpyruvate · ligand · 2 copies · chains A, B
- A5P · Arabinose-5-phosphate · ligand · 2 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
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 225 | 0.79 | 0.93 | 48 | PEP, A5P |
| 2 | 285 | 0.74 | 0.87 | 45 | PEP, A5P |
| 3 | 79 | 0.57 | 0.87 | 31 | empty |
| 4 | 108 | 0.44 | 0.78 | 20 | empty |
| 5 | 60 | 0.29 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1891 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 2A2I · Aquifex aeolicus KDO8PS in complex with PEP, A5P, Zn2+ · 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 O66496
- Elsewhere: RCSB PDB 2A2I · PDBe 2A2I · UniProt O66496
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