MolNFT v1 · #66658 · protein
Crystal structure of menaquinone synthesis protein mend from E. COLI in complex with thdp
3HWX · 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1…: “Crystal structure of menaquinone synthesis protein mend from E. COLI in complex with thdp”. X-ray diffraction, 3 ligands (TPP, NA, MG), 20 pockets (best druggability 0.86).…
- PDB
- 3HWX
- Type
- protein
- Length
- 4,441 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
- TPP, NA, MG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 41% 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 | 555 | 41% helix, 16% strand | P17109 |
| B, J, S, 1 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase (EC 2.2.1.9) | protein | 556 | 41% helix, 16% strand | P17109 |
| I, R, Z | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase (EC 2.2.1.9) | protein | 554 | 42% helix, 16% strand | P17109 |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · 8 copies · chains A, B, I, J, R, S, Z, 1
- NA · Sodium ion · metal · 15 copies · chains A, I, B, J, R, S, Z, 1
- MG · Magnesium ion · metal · 8 copies · chains A, B, I, J, R, S, Z, 1
- GOL · Glycerol · additive · 2 copies · chains J, 1
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 | 979 | 0.86 | 0.87 | 137 | empty |
| 2 | 954 | 0.86 | 0.87 | 135 | empty |
| 3 | 501 | 0.82 | 0.89 | 68 | TPP |
| 4 | 645 | 0.82 | 0.87 | 80 | empty |
| 5 | 1042 | 0.82 | 0.83 | 113 | TPP, MG |
Interfaces
15 interfaces between chains.
- R–S · 3567 Ų buried · 52 hydrogen bonds · protein-protein
- A–B · 3542 Ų buried · 49 hydrogen bonds · protein-protein
- Z–1 · 3533 Ų buried · 50 hydrogen bonds · protein-protein
- I–J · 3531 Ų buried · 51 hydrogen bonds · protein-protein
- B–J · 1637 Ų buried · 46 hydrogen bonds · protein-protein
Compared structures
- 3HWX · Crystal structure of menaqui synthesis protein MenD from E. coli in complex with ThDP · the same entry in another collection · chain 1 against 1, 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 3HWX · PDBe 3HWX · UniProt P17109
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