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Dihydrodipicolinate synthase (dhdps) from C.JEJUNI, E88Q mutant with pyruvate bound in the active site and L-lysine bound at the allosteric site
Analyse Dihydrodipicolinate synthase (dhdps) from C.JEJUNI, E88Q 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
- 7KPC
- Type
- protein
- Length
- 1,777 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
- 12 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) | protein | 295 | 49% helix, 14% strand | Q9PPB4 |
| B, D, E | 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) | protein | 296 | 49% helix, 14% strand | Q9PPB4 |
| C, F | 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) | protein | 297 | 48% helix, 14% strand | Q9PPB4 |
Ligands and binding sites
- LYS · Lysine · ligand · 6 copies · chains A, D, B, C, E, F
- MG · Magnesium ion · metal · 14 copies · chains A, B, C, D, E, F
- EDO · 1,2-ethanediol · additive · 28 copies · chains A, D, B, C, E, F
- ACT · Acetate ion · additive · 15 copies · chains A, B, C, E, D, F
- PEG · Di(hydroxyethyl)ether · additive · 12 copies · chains A, B, C, D, E, F
- PGE · Triethylene glycol · additive · 10 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · 3 copies · chains B, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 321 | 0.78 | 0.89 | 40 | LYS, MG, EDO |
| 2 | 360 | 0.78 | 0.88 | 53 | LYS, MG, PGE |
| 3 | 385 | 0.75 | 0.85 | 57 | LYS, MG, EDO, ACT |
| 4 | 696 | 0.71 | 0.78 | 57 | ACT, EDO, PEG |
| 5 | 170 | 0.52 | 0.79 | 28 | MG, ACT |
Interfaces
6 interfaces between chains.
- E–F · 1519 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1495 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 1408 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 987 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 974 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (nonstandard).
Compared structures
- 7KPC · Dihydrodipicolinate synthase (DHDPS) from C.jejuni, E88Q 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 D 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 7KPC · PDBe 7KPC · UniProt Q9PPB4
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