Research workbench
Engineering the enolase active site pocket: crystal structure of the S39N Q167K D321R mutant of yeast enolase 1
Analyse Engineering the enolase active site pocket: crystal structure of the S39N Q167K… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XH0
- Type
- protein
- Length
- 1,748 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Enolase 1
- EC
- 4.2.1.11
- UniProt
- P00924
- Ligands
- PEP, MG
- Pockets
- 15 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Enolase 1 (EC 4.2.1.11) | protein | 437 | 45% helix, 18% strand | P00924 |
Ligands and binding sites
- PEP · Phosphoenolpyruvate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1133 | 0.79 | 0.80 | 92 | empty |
| 2 | 1016 | 0.73 | 0.76 | 50 | empty |
| 3 | 948 | 0.73 | 0.77 | 51 | empty |
| 4 | 311 | 0.70 | 0.84 | 51 | PEP |
| 5 | 376 | 0.69 | 0.82 | 56 | PEP |
Interfaces
3 interfaces between chains.
- C–D · 1975 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 1936 Ų buried · 39 hydrogen bonds · protein-protein
- B–C · 376 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2XH0 · Engineering the enolase active site pocket: Crystal structure of the S39N Q167K D321R… · the same entry in another collection · chain D against D, TM-score 1.00
- P00924 · AlphaFold monomer V2.0 prediction for enolase 1 (P00924) · 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 P00924
- Elsewhere: RCSB PDB 2XH0 · PDBe 2XH0 · UniProt P00924
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