MolNFT v1 · #54182 · protein
Engineering the enolase active site pocket: crystal structure of the S39N D321A mutant of yeast enolase 1
2XH2: “Engineering the enolase active site pocket: crystal structure of the S39N D321A mutant of yeast enolase 1”. X-ray diffraction, 2 ligands (2PG, MG), 13 pockets (best druggability 0.79). MolNFT v1 #54182 on GenesisL1: 3D structure…
- PDB
- 2XH2
- 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
- 2PG, MG
- Pockets
- 13 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Enolase 1 (EC 4.2.1.11) | protein | 437 | 44% helix, 18% strand | P00924 |
Ligands and binding sites
- 2PG · 2-phosphoglyceric acid · 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
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1127 | 0.79 | 0.81 | 119 | empty |
| 2 | 907 | 0.72 | 0.77 | 54 | empty |
| 3 | 388 | 0.69 | 0.82 | 57 | 2PG |
| 4 | 348 | 0.69 | 0.83 | 57 | 2PG |
| 5 | 430 | 0.64 | 0.78 | 63 | 2PG |
Interfaces
4 interfaces between chains.
- C–D · 1960 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 1949 Ų buried · 38 hydrogen bonds · protein-protein
- A–D · 502 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 97 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2XH2 · Engineering the enolase active site pocket: Crystal structure of the S39N 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 C 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 2XH2 · PDBe 2XH2 · UniProt P00924
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