Research workbench
Ecmend-thdp-MN2+ complex soaked with 2-ketoglutarate for 1.5 H
Analyse Ecmend-thdp-MN2+ complex soaked with 2-ketoglutarate for 1.5 H in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EJ5
- Type
- protein
- Length
- 4,448 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase
- EC
- 2.2.1.9
- UniProt
- P17109
- Ligands
- TD6, MN
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase (EC 2.2.1.9) | protein | 556 | 42% helix, 16% strand | P17109 |
Ligands and binding sites
- TD6 · (4S)-4-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3lambda~5~-thiazol-2-yl}-4-hydroxybutanoic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- GOL · Glycerol · additive · 8 copies · chains A, B, 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 | 681 | 0.86 | 0.90 | 110 | TD6, MN |
| 2 | 603 | 0.85 | 0.90 | 98 | TD6, MN |
| 3 | 600 | 0.85 | 0.90 | 98 | TD6, MN |
| 4 | 818 | 0.84 | 0.87 | 134 | empty |
| 5 | 941 | 0.82 | 0.83 | 115 | TD6, MN |
Interfaces
15 interfaces between chains.
- A–B · 3528 Ų buried · 50 hydrogen bonds · protein-protein
- E–F · 3523 Ų buried · 50 hydrogen bonds · protein-protein
- C–D · 3518 Ų buried · 52 hydrogen bonds · protein-protein
- G–H · 3494 Ų buried · 52 hydrogen bonds · protein-protein
- B–D · 1577 Ų buried · 39 hydrogen bonds · protein-protein
Compared structures
- 5EJ5 · EcMenD-ThDP-Mn2+ complex soaked with 2-ketoglutarate for 1.5 h · the same entry in another collection · chain H against H, TM-score 1.00
- P17109 · AlphaFold monomer V2.0 prediction for 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-c… · a predicted model of the same protein · chain A 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 P17109
- Elsewhere: RCSB PDB 5EJ5 · PDBe 5EJ5 · UniProt P17109
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