Research workbench
Crystal structure of enolase from escherichia COLI with bound 2- phosphoglycerate substrate
Analyse Crystal structure of enolase from escherichia COLI with bound 2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BFY
- Type
- protein
- Length
- 2,630 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Enolase
- EC
- 4.2.1.11
- UniProt
- B7MLA0
- Ligands
- 2PG, MG, SO4
- Pockets
- 17 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Enolase (EC 4.2.1.11) | protein | 439 | 42% helix, 19% strand | B7MLA0 |
| B, D, E | Enolase (EC 4.2.1.11) | protein | 438 | 42% helix, 19% strand | B7MLA0 |
| F | Enolase (EC 4.2.1.11) | protein | 438 | 42% helix, 18% strand | B7MLA0 |
Ligands and binding sites
- 2PG · 2-phosphoglyceric acid · ligand · 6 copies · chains A, B, C, F, D, E
- MG · Magnesium ion · metal · 12 copies · chains A, B, C, F, D, E
- SO4 · Sulfate ion · ion · 22 copies · chains A, B, C, D, F, E
- GOL · Glycerol · additive · 3 copies · chains A, B, C, F, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1014 | 0.83 | 0.84 | 99 | GOL, SO4 |
| 2 | 529 | 0.79 | 0.85 | 59 | SO4 |
| 3 | 513 | 0.79 | 0.86 | 67 | GOL |
| 4 | 103 | 0.66 | 0.90 | 31 | GOL |
| 5 | 322 | 0.61 | 0.79 | 39 | SO4 |
Interfaces
15 interfaces between chains.
- C–D · 1998 Ų buried · 45 hydrogen bonds · protein-protein
- F–E · 1984 Ų buried · 52 hydrogen bonds · protein-protein
- A–B · 1955 Ų buried · 44 hydrogen bonds · protein-protein
- F–D · 651 Ų buried · 9 hydrogen bonds · protein-protein
- B–E · 609 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6BFY · Crystal structure of enolase from Escherichia coli with bound 2-phosphoglycerate substrate · the same entry in another collection · chain E against E, TM-score 1.00
- B7MLA0 · AlphaFold monomer V2.0 prediction for enolase (B7MLA0) · a predicted model of the same protein · chain F against A, TM-score 0.98
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 B7MLA0
- Elsewhere: RCSB PDB 6BFY · PDBe 6BFY · UniProt B7MLA0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.