Research workbench
Fluoride inhibition of enolase: crystal structure of the inhibitory complex
Analyse Fluoride inhibition of enolase: crystal structure of the inhibitory complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2AKZ
- Type
- protein
- Length
- 867 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gamma enolase
- EC
- 4.2.1.11
- UniProt
- P09104
- Ligands
- MG, F, PO4
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gamma enolase (EC 4.2.1.11) | protein | 435 | 45% helix, 17% strand | P09104 |
| B | Gamma enolase (EC 4.2.1.11) | protein | 432 | 44% helix, 17% strand | P09104 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B
- F · Fluoride ion · ion · 4 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1058 | 0.74 | 0.77 | 61 | empty |
| 2 | 242 | 0.53 | 0.77 | 36 | empty |
| 3 | 210 | 0.51 | 0.77 | 34 | empty |
| 4 | 66 | 0.37 | 0.78 | 18 | empty |
| 5 | 82 | 0.33 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2059 Ų buried · 49 hydrogen bonds · protein-protein
Compared structures
- 2AKZ · Fluoride Inhibition of Enolase: Crystal Structure of the Inhibitory Complex · the same entry in another collection · chain A against A, TM-score 1.00
- P09104 · AlphaFold monomer V2.0 prediction for gamma-enolase (P09104) · a predicted model of the same protein · chain B 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 P09104
- Elsewhere: RCSB PDB 2AKZ · PDBe 2AKZ · UniProt P09104
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