MolNFT v1 · #5230 · protein
Chelation of ser 39 to MG2+ latches a gate at the active site of enolase: structure of the BIS(MG2+) complex of yeast enolase and the intermediate analog phosphonoacetohydroxamate at 2.1 ångströms resolution
1EBG: “Chelation of ser 39 to MG2+ latches a gate at the active site of enolase: structure of the BIS(MG2+) complex…”. X-ray diffraction, 2 ligands (PAH, MG), 7 pockets (best druggability 0.70). MolNFT v1 #5230 on GenesisL1: 3D structure…
- PDB
- 1EBG
- Type
- protein
- Length
- 872 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Enolase
- EC
- 4.2.1.11
- UniProt
- P00924
- Ligands
- PAH, MG
- Pockets
- 7 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Enolase (EC 4.2.1.11) | protein | 436 | 45% helix, 17% strand | P00924 |
Ligands and binding sites
- PAH · Phosphonoacetohydroxamic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
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 | 840 | 0.70 | 0.76 | 48 | empty |
| 2 | 173 | 0.51 | 0.78 | 26 | empty |
| 3 | 201 | 0.50 | 0.77 | 34 | empty |
| 4 | 78 | 0.41 | 0.78 | 22 | empty |
| 5 | 97 | 0.40 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2004 Ų buried · 41 hydrogen bonds · protein-protein
Compared structures
- 1EBG · Chelation of ser 39 to MG2+ latches a gate at the active site of enolase: structure of… · the same entry in another collection · chain A against A, TM-score 1.00
- P00924 · AlphaFold monomer V2.0 prediction for enolase 1 (P00924) · a predicted model of the same protein · chain B 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 1EBG · PDBe 1EBG · UniProt P00924
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