Research workbench
Structure of the menaquinone biosynthesis protein mend from bacillus subtilis
Analyse Structure of the menaquinone biosynthesis protein mend from bacillus subtilis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2X7J
- Type
- protein
- Length
- 2,314 residues
- Chains
- 4
- 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
- P23970
- Ligands
- TPP, MN, NA, SO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene -1-carboxylate synthase (EC 2.2.1.9) | protein | 579 | 45% helix, 16% strand | P23970 |
| C | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene -1-carboxylate synthase (EC 2.2.1.9) | protein | 577 | 44% helix, 16% strand | P23970 |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 324 | 0.83 | 0.94 | 64 | TPP, MN, EDO |
| 2 | 334 | 0.83 | 0.92 | 58 | EDO, TPP, MN |
| 3 | 228 | 0.82 | 0.95 | 50 | EDO, TPP, MN |
| 4 | 361 | 0.81 | 0.90 | 40 | empty |
| 5 | 221 | 0.79 | 0.93 | 45 | empty |
Interfaces
6 interfaces between chains.
- C–D · 3318 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 3303 Ų buried · 38 hydrogen bonds · protein-protein
- B–C · 1731 Ų buried · 35 hydrogen bonds · protein-protein
- A–D · 1712 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 765 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 2X7J · Structure of the menaqui biosynthesis protein MenD from Bacillus subtilis · the same entry in another collection · chain A against A, TM-score 1.00
- P23970 · 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 P23970
- Elsewhere: RCSB PDB 2X7J · PDBe 2X7J · UniProt P23970
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