MolNFT v1 · #66657 · protein
Crystal structure of menaquinone synthesis protein mend from E. COLI in complex with oxoglutarate
3HWW · 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1…: “Crystal structure of menaquinone synthesis protein mend from E. COLI in complex with oxoglutarate”. X-ray diffraction, 4 ligands (AKG, NA, MG), 11 pockets (best druggability…
- PDB
- 3HWW
- Type
- protein
- Length
- 1,071 residues
- Chains
- 2
- 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
- AKG, NA, MG, CL
- Pockets
- 11 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase (EC 2.2.1.9) | protein | 539 | 40% helix, 16% strand | P17109 |
| D | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase (EC 2.2.1.9) | protein | 532 | 41% helix, 16% strand | P17109 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 2 copies · chains A, D
- NA · Sodium ion · metal · 37 copies · chains A, D
- MG · Magnesium ion · metal · 2 copies · chains A, D
- CL · Chloride ion · ion · 2 copies · chains A, D
- GOL · Glycerol · additive · 6 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 671 | 0.69 | 0.77 | 71 | NA, AKG, MG |
| 2 | 543 | 0.66 | 0.77 | 55 | AKG, MG, GOL |
| 3 | 380 | 0.66 | 0.80 | 38 | NA |
| 4 | 304 | 0.64 | 0.81 | 42 | CL |
| 5 | 192 | 0.61 | 0.83 | 34 | empty |
Interfaces
1 interface between chains.
- A–D · 2667 Ų buried · 45 hydrogen bonds · protein-protein
Compared structures
- 3HWW · Crystal structure of menaqui synthesis protein MenD from E. coli in complex with… · the same entry in another collection · chain A against A, 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 D 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 3HWW · PDBe 3HWW · UniProt P17109
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