Research workbench
Dihydrodipicolinate synthase (DHDPS) from C.jejuni, E88Q mutant with pyruvate bound in the active site and R,R-bislysine 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
- 7KPE
- Type
- protein
- Length
- 1,772 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.06
- Source
- Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC…
- Molecule
- 4-hydroxy-tetrahydrodipicolinate synthase
- EC
- 4.3.3.7
- UniProt
- Q9PPB4
- Ligands
- 3VN, MG
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · resolution 2.06 · 3 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, F | 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) | protein | 296 | 48% helix, 14% strand | Q9PPB4 |
| D | 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) | protein | 293 | 48% helix, 14% strand | Q9PPB4 |
| E | 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 · 3 copies · chains B, C, A, D, E, F
- MG · Magnesium ion · metal · 7 copies · chains A, B, C, D, E
- ACT · Acetate ion · additive · 7 copies · chains A, C, E, D, F
- PGE · Triethylene glycol · additive · 4 copies · chains A, B, E, F
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, F
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains C, D
- GOL · Glycerol · additive · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 531 | 0.76 | 0.84 | 65 | MG, 3VN, ACT |
| 2 | 468 | 0.76 | 0.85 | 58 | 3VN, MG |
| 3 | 490 | 0.75 | 0.83 | 63 | 3VN, MG |
| 4 | 575 | 0.68 | 0.78 | 54 | ACT |
| 5 | 215 | 0.54 | 0.78 | 26 | empty |
Interfaces
6 interfaces between chains.
- E–F · 1417 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 1415 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 1414 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1015 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 982 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (nonstandard).
Compared structures
- 7KPE · 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 7KPE · PDBe 7KPE · UniProt Q9PPB4
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