MolNFT v1 · #180345 · protein
Dihydrodipicolinate synthase from C. jejuni with pyruvate bound to the active site in C2221 space group
7KWN · 4-hydroxy-tetrahydrodipicolinate synthase: “Dihydrodipicolinate synthase from C. jejuni with pyruvate bound to the active site in C2221 space group”. X-ray diffraction, 1 ligand (MG), 13 pockets (best druggability 0.74). MolNFT v1…
- 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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