Research workbench
Dihydrodipicolinate synthase (dhdps) from C.JEJUNI, H56W mutant with pyruvate bound in the active site and L-lysine bound at the allosteric site
Analyse Dihydrodipicolinate synthase (dhdps) from C.JEJUNI, H56W mutant with pyruvate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KG9
- Type
- protein
- Length
- 1,784 residues
- Chains
- 6
- 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
- LYS, MG
- Pockets
- 14 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) | protein | 295 | 47% helix, 14% strand | Q9PPB4 |
| B, C, E | 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) | protein | 296 | 47% helix, 14% strand | Q9PPB4 |
| D | 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) | protein | 304 | 45% helix, 13% strand | Q9PPB4 |
| F | 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) | protein | 297 | 46% helix, 13% strand | Q9PPB4 |
Ligands and binding sites
- LYS · Lysine · ligand · 6 copies · chains A, E, B, C, D, F
- MG · Magnesium ion · metal · 7 copies · chains B, C, D, F
- EDO · 1,2-ethanediol · additive · 17 copies · chains A, B, C, D, F
- PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains A, E, B, C, D, F
- PGE · Triethylene glycol · additive · 3 copies · chains A, D, F
- GOL · Glycerol · additive · 2 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 265 | 0.77 | 0.90 | 49 | EDO, PEG, LYS |
| 2 | 230 | 0.77 | 0.90 | 39 | LYS |
| 3 | 218 | 0.75 | 0.90 | 38 | LYS, EDO |
| 4 | 677 | 0.70 | 0.78 | 59 | empty |
| 5 | 222 | 0.55 | 0.78 | 25 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1560 Ų buried · 18 hydrogen bonds · protein-protein
- D–F · 1546 Ų buried · 15 hydrogen bonds · protein-protein
- A–E · 1522 Ų buried · 17 hydrogen bonds · protein-protein
- C–E · 1051 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1023 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (nonstandard).
Compared structures
- 7KG9 · Dihydrodipicolinate synthase (DHDPS) from C.jejuni, H56W mutant with pyruvate bound in… · the same entry in another collection · chain F against F, 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 7KG9 · PDBe 7KG9 · UniProt Q9PPB4
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