Research workbench
Crystal structure of escherichia COLI enolase complexed with a natural inhibitor SF2312.
Analyse Crystal structure of escherichia COLI enolase complexed with a natural… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6D3Q
- 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
- 4NG, MG, SO4
- Pockets
- 18 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Enolase (EC 4.2.1.11) | protein | 438 | 41% helix, 19% strand | B7MLA0 |
| C | Enolase (EC 4.2.1.11) | protein | 437 | 42% helix, 18% strand | B7MLA0 |
| E, F, D | Enolase (EC 4.2.1.11) | protein | 439 | 42% helix, 19% strand | B7MLA0 |
Ligands and binding sites
- 4NG · [(3S,5S)-1,5-dihydroxy-2-oxopyrrolidin-3-yl]phosphonic acid · ligand · 6 copies · chains A, C, B, E, F, D
- MG · Magnesium ion · metal · 12 copies · chains A, C, B, E, F, D
- SO4 · Sulfate ion · ion · 12 copies · chains A, C, B, F, D, E
- GOL · Glycerol · additive · 5 copies · chains A, B, E, F, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1021 | 0.83 | 0.84 | 96 | SO4 |
| 2 | 967 | 0.82 | 0.83 | 74 | empty |
| 3 | 900 | 0.81 | 0.83 | 69 | empty |
| 4 | 485 | 0.72 | 0.82 | 53 | empty |
| 5 | 482 | 0.72 | 0.82 | 54 | empty |
Interfaces
15 interfaces between chains.
- A–B · 1969 Ų buried · 46 hydrogen bonds · protein-protein
- C–D · 1948 Ų buried · 38 hydrogen bonds · protein-protein
- E–F · 1907 Ų buried · 36 hydrogen bonds · protein-protein
- E–D · 608 Ų buried · 9 hydrogen bonds · protein-protein
- A–F · 606 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6D3Q · Crystal structure of Escherichia coli enolase complexed with a natural inhibitor SF2312. · the same entry in another collection · chain D against D, TM-score 1.00
- B7MLA0 · AlphaFold monomer V2.0 prediction for enolase (B7MLA0) · a predicted model of the same protein · chain A 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 6D3Q · PDBe 6D3Q · UniProt B7MLA0
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