MolNFT v1 · #118439 · protein
Biomimetic design results in a potent allosteric inhibitor of dihydrodipicolinate synthase from campylobacter jejuni
5F1V · 4-hydroxy-tetrahydrodipicolinate synthase: “Biomimetic design results in a potent allosteric inhibitor of dihydrodipicolinate synthase from campylobacter…”. X-ray diffraction, 1 ligand (3VN), 9 pockets (best druggability 0.73).…
- PDB
- 5F1V
- Type
- protein
- Length
- 1,184 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-hydroxy-tetrahydrodipicolinate synthase
- EC
- 4.3.3.7
- UniProt
- Q9PPB4
- Ligands
- 3VN
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) | protein | 296 | 47% helix, 14% strand | Q9PPB4 |
| B | 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) | protein | 297 | 48% helix, 14% strand | Q9PPB4 |
| D | 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) | protein | 295 | 47% helix, 14% strand | Q9PPB4 |
Ligands and binding sites
- 3VN · (2R,5R)-2,5-diamino-2,5-bis(4-aminobutyl)hexanedioic acid · ligand · 4 copies · chains A, C, B, D
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B, C, D
- PGE · Triethylene glycol · additive · 3 copies · chains A, B, D
- GOL · Glycerol · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 214 | 0.73 | 0.89 | 37 | 3VN |
| 2 | 221 | 0.70 | 0.87 | 29 | 3VN |
| 3 | 185 | 0.52 | 0.78 | 24 | empty |
| 4 | 182 | 0.52 | 0.78 | 25 | empty |
| 5 | 168 | 0.52 | 0.79 | 24 | empty |
Interfaces
4 interfaces between chains.
- B–D · 1525 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1503 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 1047 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1010 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 5F1V · biomimetic design results in a potent allosteric inhibitor of dihydrodipicolinate… · the same entry in another collection · chain D against D, TM-score 1.00
- Q9PPB4 · AlphaFold monomer V2.0 prediction for 4-hydroxy- tetrahydrodipicolinate synthase (Q9PPB4) · a predicted model of the same protein · chain B against A, TM-score 1.00
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 Q9PPB4
- Elsewhere: RCSB PDB 5F1V · PDBe 5F1V · UniProt Q9PPB4
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