MolNFT v1 · #46774 · protein
Crystal structure of a rubisco-like protein from geobacillus kaustophilus liganded with MG2+ and 2,3-diketohexane 1-phosphate
2OEM · 2,3-diketo-5-methylthiopentyl-1-phosphate enolase: “Crystal structure of a rubisco-like protein from geobacillus kaustophilus liganded with MG2+ and…”. X-ray diffraction, 2 ligands (1AE, MG), 6 pockets (best druggability 0.77).…
- PDB
- 2OEM
- Type
- protein
- Length
- 820 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2,3-diketo-5-methylthiopentyl-1-phosphate enolase
- EC
- 5.3.2.-
- UniProt
- Q5L1E2
- Ligands
- 1AE, MG
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2,3-diketo-5-methylthiopentyl-1-phosphate enolase (EC 5.3.2.-) | protein | 408 | 46% helix, 17% strand | Q5L1E2 |
| B | 2,3-diketo-5-methylthiopentyl-1-phosphate enolase (EC 5.3.2.-) | protein | 412 | 46% helix, 17% strand | Q5L1E2 |
Ligands and binding sites
- 1AE · (1Z)-2-hydroxy-3-oxohex-1-en-1-yl dihydrogen phosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 87 | 0.77 | 0.98 | 29 | empty |
| 2 | 512 | 0.69 | 0.79 | 52 | MG, 1AE |
| 3 | 406 | 0.66 | 0.79 | 52 | MG, 1AE |
| 4 | 299 | 0.59 | 0.78 | 56 | empty |
| 5 | 60 | 0.34 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 3092 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (carboxylation).
Compared structures
- 2OEM · Crystal structure of a rubisco-like protein from Geobacillus kaustophilus liganded with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q5L1E2 · AlphaFold monomer V2.0 prediction for 2,3-diketo-5-methylthiopentyl-1-phosphate enolase… · a predicted model of the same protein · chain A 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 Q5L1E2
- Elsewhere: RCSB PDB 2OEM · PDBe 2OEM · UniProt Q5L1E2
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