Research workbench
Crystal structure of menaquinone synthesis protein mend from E. COLI in complex with thdp
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
- 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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.