MolNFT v1 · #118184 · protein
Structure of human enolase 2 in complex with ((3S,5S)-1,5-dihydroxy-3- methyl-2-oxopyrrolidin-3-YL)PHOSPHONIC acid
5EU9 · Gamma-enolase: “Structure of human enolase 2 in complex with ((3S,5S)-1,5-dihydroxy-3- methyl-2-oxopyrrolidin-3-YL)PHOSPHONIC…”. X-ray diffraction, 2 ligands (5TX, MG), 20 pockets (best druggability 0.82). MolNFT v1 #118184 on…
- PDB
- 5EU9
- Type
- protein
- Length
- 3,468 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gamma-enolase
- EC
- 4.2.1.11
- UniProt
- P09104
- Ligands
- 5TX, MG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, G, H | Gamma-enolase (EC 4.2.1.11) | protein | 433 | 42% helix, 17% strand | P09104 |
| C | Gamma-enolase (EC 4.2.1.11) | protein | 436 | 44% helix, 17% strand | P09104 |
| F | Gamma-enolase (EC 4.2.1.11) | protein | 434 | 43% helix, 17% strand | P09104 |
Ligands and binding sites
- 5TX · ((3S,5S)-1,5-dihydroxy-3-methyl-2-oxopyrrolidin-3-yl)phosphonic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- MG · Magnesium ion · metal · 16 copies · chains A, B, C, D, E, F, G, H
- PGE · Triethylene glycol · additive · 6 copies · chains C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1076 | 0.82 | 0.83 | 87 | empty |
| 2 | 1191 | 0.76 | 0.79 | 88 | empty |
| 3 | 92 | 0.75 | 0.97 | 26 | MG, 5TX |
| 4 | 1107 | 0.74 | 0.77 | 61 | PGE |
| 5 | 88 | 0.74 | 0.97 | 25 | MG, 5TX |
Interfaces
8 interfaces between chains.
- A–B · 2092 Ų buried · 43 hydrogen bonds · protein-protein
- E–F · 2087 Ų buried · 43 hydrogen bonds · protein-protein
- G–H · 2012 Ų buried · 41 hydrogen bonds · protein-protein
- C–D · 1983 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 631 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5EU9 · Structure of Human Enolase 2 in complex with ((3S,5S)-1,5-dihydroxy-3-methyl-2-oxopyrrolid… · the same entry in another collection · chain H against H, TM-score 1.00
- P09104 · AlphaFold monomer V2.0 prediction for gamma-enolase (P09104) · a predicted model of the same protein · chain D against A, TM-score 1.00
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 P09104
- Elsewhere: RCSB PDB 5EU9 · PDBe 5EU9 · UniProt P09104
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