Research workbench
Dihydrodipicolinate synthase (dhdps) from C.JEJUNI, H59A mutant with pyruvate bound in the active site
Analyse Dihydrodipicolinate synthase (dhdps) from C.JEJUNI, H59A 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
- 7KLQ
- Type
- protein
- Length
- 1,776 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
- MG
- Pockets
- 12 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) | protein | 296 | 48% helix, 14% strand | Q9PPB4 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, E
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B, C, D, F, E
- PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains A, B, C, D, F
- PGE · Triethylene glycol · additive · 4 copies · chains A, B, D
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 551 | 0.79 | 0.85 | 68 | empty |
| 2 | 555 | 0.79 | 0.85 | 66 | EDO |
| 3 | 525 | 0.78 | 0.85 | 62 | empty |
| 4 | 538 | 0.68 | 0.78 | 54 | empty |
| 5 | 201 | 0.52 | 0.77 | 28 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1457 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 1445 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 1440 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1020 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 984 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (nonstandard).
Compared structures
- 7KLQ · Dihydrodipicolinate synthase (DHDPS) from C.jejuni, H59A 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 7KLQ · PDBe 7KLQ · UniProt Q9PPB4
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