Research workbench
Aquifex aeolicus KDO8PS R106G mutant in complex with 2PGA and R5P
Analyse Aquifex aeolicus KDO8PS R106G mutant in complex with 2PGA and R5P in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZJI
- Type
- protein
- Length
- 513 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
- 2PG, R5P, CD, PO4
- Pockets
- 5 · best druggability 0.78
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 | 257 | 42% helix, 20% strand | O66496 |
| B | 2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55) | protein | 256 | 42% helix, 20% strand | O66496 |
Ligands and binding sites
- 2PG · 2-phosphoglyceric acid · ligand · 2 copies · chains A, B
- R5P · Ribose-5-phosphate · ligand · chains A
- CD · Cadmium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains 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 | 397 | 0.78 | 0.87 | 44 | R5P, 2PG |
| 2 | 386 | 0.78 | 0.87 | 47 | PO4, 2PG |
| 3 | 84 | 0.57 | 0.87 | 26 | empty |
| 4 | 112 | 0.43 | 0.77 | 21 | empty |
| 5 | 55 | 0.28 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1704 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 1ZJI · Aquifex aeolicus KDO8PS R106G mutant in complex with 2PGA and R5P · 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 1ZJI · PDBe 1ZJI · UniProt O66496
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