MolNFT v1 · #117806 · protein
Ecmend-thdp-MN2+ complex structure soaked with 2-ketoglutarate for 2 min
5EJ8 · 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1…: “Ecmend-thdp-MN2+ complex structure soaked with 2-ketoglutarate for 2 min”. X-ray diffraction, 3 ligands (TD6, MG, MN), 20 pockets (best druggability 0.82). MolNFT v1 #117806 on…
- PDB
- 5EJ8
- 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, MG, MN
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 41% 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 | 41% 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
- MG · Magnesium ion · metal · 15 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
- FMT · Formic acid · additive · 45 copies · chains A, B, C, D, E, F, G, H
- EDO · 1,2-ethanediol · additive · 21 copies · chains A, B, C, D, E, F, G, H
- GOL · Glycerol · additive · 14 copies · chains A, B, C, D, E, F, G, H
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains C
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 | 744 | 0.82 | 0.85 | 87 | FMT, TD6 |
| 2 | 621 | 0.82 | 0.87 | 99 | empty |
| 3 | 722 | 0.81 | 0.85 | 88 | TD6, MN, MG, FMT |
| 4 | 778 | 0.81 | 0.84 | 86 | FMT, TD6, MN, MG, EDO |
| 5 | 803 | 0.81 | 0.84 | 86 | TD6, EDO, FMT |
Interfaces
15 interfaces between chains.
- A–B · 3534 Ų buried · 59 hydrogen bonds · protein-protein
- G–H · 3520 Ų buried · 58 hydrogen bonds · protein-protein
- C–D · 3513 Ų buried · 59 hydrogen bonds · protein-protein
- E–F · 3511 Ų buried · 56 hydrogen bonds · protein-protein
- E–G · 1525 Ų buried · 39 hydrogen bonds · protein-protein
Compared structures
- 5EJ8 · EcMenD-ThDP-Mn2+ complex structure soaked with 2-ketoglutarate for 2 min · 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 5EJ8 · PDBe 5EJ8 · UniProt P17109
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