MolNFT v1 · #61954 · protein
CU2+ substituted aquifex aeolicus KDO8PS in complex with KDO8P
3E12 · 2-dehydro-3-deoxyphosphooctonate aldolase: “CU2+ substituted aquifex aeolicus KDO8PS in complex with KDO8P”. X-ray diffraction, 3 ligands (KD0, CU, PO4), 5 pockets (best druggability 0.75). MolNFT v1 #61954 on GenesisL1: 3D…
- PDB
- 3E12
- Type
- protein
- Length
- 514 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
- KD0, CU, PO4
- Pockets
- 5 · best druggability 0.75
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 | 258 | 43% 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
- KD0 · 3-deoxy-8-O-phosphono-D-manno-oct-2-ulosonic acid · ligand · 2 copies · chains A, B
- CU · Copper (II) ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- ACT · Acetate ion · additive · 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 | 291 | 0.75 | 0.88 | 49 | KD0, PO4 |
| 2 | 260 | 0.74 | 0.88 | 46 | KD0, PO4 |
| 3 | 58 | 0.64 | 0.94 | 25 | empty |
| 4 | 75 | 0.33 | 0.75 | 19 | empty |
| 5 | 59 | 0.30 | 0.75 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 1898 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 3E12 · Cu2+ substituted Aquifex aeolicus KDO8PS in complex with KDO8P · 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 3E12 · PDBe 3E12 · UniProt O66496
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