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Crystal structure of menaquinone synthesis protein mend from E. COLI in complex with oxoglutarate
Analyse Crystal structure of menaquinone synthesis protein mend from E. COLI in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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