MolNFT v1 · #191420 · protein
Crystal structure of 2,3-diketo-5-methylthiopentyl-1-phosphate enolase-phosphatase from klebsiella aerogenes (P21 form)
8DOQ · 2,3-diketo-5-methylthiopentyl-1-phosphate enolase…: “Crystal structure of 2,3-diketo-5-methylthiopentyl-1-phosphate enolase-phosphatase from klebsiella aerogenes…”. X-ray diffraction, 1 ligand (BEZ), 5 pockets (best druggability…
- PDB
- 8DOQ
- Type
- protein
- Length
- 437 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2,3-diketo-5-methylthiopentyl-1-phosphate enolase- phosphatase
- EC
- 4.1.1.23
- UniProt
- A0A0M3H420
- Ligands
- BEZ
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2,3-diketo-5-methylthiopentyl-1-phosphate enolase- phosphatase (EC 4.1.1.23) | protein | 218 | 51% helix, 17% strand | A0A0M3H420 |
| B | 2,3-diketo-5-methylthiopentyl-1-phosphate enolase- phosphatase (EC 4.1.1.23) | protein | 219 | 50% helix, 17% strand | A0A0M3H420 |
Ligands and binding sites
- BEZ · Benzoic acid · ligand · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 121 | 0.80 | 0.98 | 26 | empty |
| 2 | 51 | 0.73 | 1.00 | 14 | BEZ |
| 3 | 507 | 0.71 | 0.80 | 53 | MPD |
| 4 | 221 | 0.68 | 0.85 | 38 | MPD |
| 5 | 106 | 0.39 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1879 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 8DOQ · Crystal structure of 2,3-diketo-5-methylthiopentyl-1-phosphate enolase-phosphatase from… · 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 A0A0M3H420
- Elsewhere: RCSB PDB 8DOQ · PDBe 8DOQ · UniProt A0A0M3H420
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