Research workbench
Dihydrodipicolinate synthase (dhdps) from C.JEJUNI, E88D mutant with pyruvate bound in the active site
Analyse Dihydrodipicolinate synthase (dhdps) from C.JEJUNI, E88D 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
- 7KO1
- 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
- MG
- Pockets
- 13 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E, F | 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 | 297 | 47% helix, 14% strand | Q9PPB4 |
Ligands and binding sites
- MG · Magnesium ion · metal · 9 copies · chains A, B, C, E, F
- ACT · Acetate ion · additive · 6 copies · chains A, B, D, E, F
- PGE · Triethylene glycol · additive · 5 copies · chains A, B, C, D, E
- EDO · 1,2-ethanediol · additive · 2 copies · chains B, C, E, F
- PEG · Di(hydroxyethyl)ether · additive · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 573 | 0.74 | 0.81 | 63 | MG, EDO |
| 2 | 492 | 0.74 | 0.82 | 60 | EDO |
| 3 | 461 | 0.72 | 0.82 | 58 | empty |
| 4 | 673 | 0.69 | 0.77 | 60 | empty |
| 5 | 169 | 0.50 | 0.78 | 23 | ACT |
Interfaces
6 interfaces between chains.
- E–F · 1393 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1372 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 1370 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1030 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 997 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (nonstandard).
Compared structures
- 7KO1 · Dihydrodipicolinate synthase (DHDPS) from C.jejuni, E88D 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 7KO1 · PDBe 7KO1 · UniProt Q9PPB4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.