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Structure of human enolase 2 in complex with (S)-(1-hydroxy-2- oxopiperidin-3-YL)PHOSPHONATE
Analyse Structure of human enolase 2 in complex with (S)-(1-hydroxy-2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IDZ
- Type
- protein
- Length
- 870 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gamma-enolase
- EC
- 4.2.1.11
- UniProt
- P09104
- Ligands
- 6BM, MG
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gamma-enolase (EC 4.2.1.11) | protein | 436 | 43% helix, 17% strand | P09104 |
| B | Gamma-enolase (EC 4.2.1.11) | protein | 434 | 43% helix, 18% strand | P09104 |
Ligands and binding sites
- 6BM · [(3S)-1-hydroxy-2-oxopiperidin-3-yl]phosphonic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PGE · Triethylene glycol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 488 | 0.74 | 0.83 | 71 | 6BM |
| 2 | 1042 | 0.74 | 0.77 | 58 | empty |
| 3 | 191 | 0.69 | 0.88 | 38 | 6BM |
| 4 | 206 | 0.53 | 0.78 | 35 | empty |
| 5 | 55 | 0.46 | 0.85 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2014 Ų buried · 42 hydrogen bonds · protein-protein
Compared structures
- 5IDZ · Structure of Human Enolase 2 in complex with (S)-(1-hydroxy-2-oxopiperidin-3-yl)phosphonat… · the same entry in another collection · chain A against A, TM-score 1.00
- P09104 · AlphaFold monomer V2.0 prediction for gamma-enolase (P09104) · 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 P09104
- Elsewhere: RCSB PDB 5IDZ · PDBe 5IDZ · UniProt P09104
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