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Dihydrodipicolinate synthase from C. jejuni with pyruvate bound to the active site
Analyse Dihydrodipicolinate synthase from C. jejuni with pyruvate bound to the active… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LY8
- Type
- protein
- Length
- 1,190 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
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) | protein | 298 | 48% helix, 14% strand | Q9PPB4 |
| B, D | 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) | protein | 297 | 48% helix, 14% strand | Q9PPB4 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 21 copies · chains A, B, C, D
- PGE · Triethylene glycol · additive · 11 copies · chains A, C, B, D
- GOL · Glycerol · additive · 5 copies · chains A, B, D
- ACT · Acetate ion · additive · 3 copies · chains A, C
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 395 | 0.76 | 0.86 | 51 | GOL |
| 2 | 403 | 0.76 | 0.85 | 52 | GOL |
| 3 | 200 | 0.52 | 0.77 | 24 | empty |
| 4 | 167 | 0.51 | 0.78 | 23 | GOL |
| 5 | 147 | 0.49 | 0.79 | 23 | EDO |
Interfaces
4 interfaces between chains.
- A–C · 1490 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 1481 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1046 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 985 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 4LY8 · dihydrodipicolinate synthase from C. jejuni with pyruvate bound to the active site · 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 4LY8 · PDBe 4LY8 · UniProt Q9PPB4
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