Research workbench
Crystal structure of a rubisco-like protein from geobacillus kaustophilus liganded with MG2+ ions
Analyse Crystal structure of a rubisco-like protein from geobacillus kaustophilus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OEK
- Type
- protein
- Length
- 824 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
- MG
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 2,3-diketo-5-methylthiopentyl-1-phosphate enolase (EC 5.3.2.-) | protein | 412 | 46% helix, 17% strand | Q5L1E2 |
Ligands and binding sites
- 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
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 | 83 | 0.77 | 0.98 | 25 | empty |
| 2 | 904 | 0.75 | 0.78 | 107 | MG |
| 3 | 464 | 0.69 | 0.80 | 41 | empty |
| 4 | 87 | 0.40 | 0.78 | 19 | empty |
| 5 | 60 | 0.35 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 3024 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (carboxylation).
Compared structures
- 2OEK · 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 2OEK · PDBe 2OEK · UniProt Q5L1E2
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