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Dihydrodipicolinate synthase from C. jejuni with pyruvate bound to the active site in C2221 space group
Analyse Dihydrodipicolinate synthase from C. jejuni with pyruvate bound to the active… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KWN
- Type
- protein
- Length
- 1,778 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 · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E | 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) | protein | 296 | 48% helix, 14% strand | Q9PPB4 |
| D, F | 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) | protein | 297 | 48% helix, 14% strand | Q9PPB4 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains B
- ACT · Acetate ion · additive · 7 copies · chains A, C, B, D, E
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B, C, D, F
- PGE · Triethylene glycol · additive · 6 copies · chains A, B, C, D, E, F
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains B, D, C, E, F
- GOL · Glycerol · additive · 3 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 409 | 0.74 | 0.84 | 60 | empty |
| 2 | 404 | 0.73 | 0.83 | 57 | ACT |
| 3 | 375 | 0.73 | 0.84 | 55 | ACT, PEG, MG |
| 4 | 625 | 0.69 | 0.77 | 59 | ACT, PEG |
| 5 | 187 | 0.54 | 0.79 | 28 | MG, EDO |
Interfaces
6 interfaces between chains.
- E–F · 1421 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1389 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 1384 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1004 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 992 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (nonstandard).
Compared structures
- 7KWN · Dihydrodipicolinate synthase from C. jejuni with pyruvate bound to the active site 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 A 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 7KWN · PDBe 7KWN · UniProt Q9PPB4
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