Research workbench
Engineering the enolase active site pocket: crystal structure of the S39A D321A mutant of yeast enolase 1
Analyse Engineering the enolase active site pocket: crystal structure of the S39A D321A… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XH4
- Type
- protein
- Length
- 1,702 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
- 2PG, MG
- Pockets
- 12 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Enolase 1 (EC 4.2.1.11) | protein | 437 | 45% helix, 18% strand | P00924 |
| B, D | Enolase 1 (EC 4.2.1.11) | protein | 414 | 47% helix, 19% strand | P00924 |
Ligands and binding sites
- 2PG · 2-phosphoglyceric acid · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 976 | 0.74 | 0.78 | 52 | empty |
| 2 | 1002 | 0.74 | 0.77 | 55 | empty |
| 3 | 196 | 0.52 | 0.77 | 35 | empty |
| 4 | 210 | 0.49 | 0.76 | 33 | empty |
| 5 | 201 | 0.47 | 0.75 | 32 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1833 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 1820 Ų buried · 37 hydrogen bonds · protein-protein
- A–C · 332 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2XH4 · Engineering the enolase active site pocket: Crystal structure of the S39A D321A mutant of… · 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 2XH4 · PDBe 2XH4 · UniProt P00924
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