Research workbench
Dihydrodipicolinate synthase (dhdps) from C.JEJUNI, N84D mutant with pyruvate bound in the active site and L-lysine bound at the allosteric site
Analyse Dihydrodipicolinate synthase (dhdps) from C.JEJUNI, N84D 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
- 7KKG
- Type
- protein
- Length
- 1,796 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, NA
- Pockets
- 13 · best druggability 0.72
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 | 297 | 46% helix, 14% strand | Q9PPB4 |
| B, D | 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) | protein | 306 | 45% helix, 13% strand | Q9PPB4 |
| C | 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) | protein | 295 | 48% helix, 14% strand | Q9PPB4 |
| E, F | 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) | protein | 296 | 46% helix, 14% strand | Q9PPB4 |
Ligands and binding sites
- LYS · Lysine · ligand · 6 copies · chains A, D, B, E, C, F
- MG · Magnesium ion · metal · 21 copies · chains A, B, C, F, D, E
- NA · Sodium ion · metal · 3 copies · chains A, C, B
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B, C, E, F
- PEG · Di(hydroxyethyl)ether · additive · 7 copies · chains A, D, B, E, C, F
- PGE · Triethylene glycol · additive · 4 copies · chains A, C, F
- PG4 · Tetraethylene glycol · additive · 3 copies · chains A, B, D
- ACT · Acetate ion · additive · 2 copies · chains E, F
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 210 | 0.72 | 0.88 | 37 | LYS, MG |
| 2 | 228 | 0.71 | 0.87 | 39 | MG, LYS |
| 3 | 188 | 0.68 | 0.87 | 27 | LYS |
| 4 | 218 | 0.57 | 0.79 | 29 | ACT |
| 5 | 203 | 0.56 | 0.79 | 29 | empty |
Interfaces
5 interfaces between chains.
- B–E · 1503 Ų buried · 15 hydrogen bonds · protein-protein
- C–F · 1495 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 1494 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 991 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 971 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (nonstandard).
Compared structures
- 7KKG · Dihydrodipicolinate synthase (DHDPS) from C.jejuni, N84D mutant with pyruvate bound in… · the same entry in another collection · chain E against E, TM-score 1.00
- Q9PPB4 · AlphaFold monomer V2.0 prediction for 4-hydroxy- tetrahydrodipicolinate synthase (Q9PPB4) · a predicted model of the same protein · chain C 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 7KKG · PDBe 7KKG · UniProt Q9PPB4
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