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Dihydrodipicolinate synthase (dhdps) from C.JEJUNI with pyruvate bound in the active site and L-lysine bound at the allosteric site in C2221 space group
Analyse Dihydrodipicolinate synthase (dhdps) from C.JEJUNI with pyruvate bound in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KWP
- 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
- LYS, MG
- Pockets
- 13 · best druggability 0.73
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
- LYS · Lysine · ligand · 6 copies · chains A, D, B, C, E, F
- MG · Magnesium ion · metal · 6 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 5 copies · chains B, A, D, E
- PEG · Di(hydroxyethyl)ether · additive · chains C
- PGE · Triethylene glycol · additive · chains 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 | 213 | 0.73 | 0.89 | 37 | LYS |
| 2 | 191 | 0.70 | 0.88 | 26 | LYS |
| 3 | 193 | 0.69 | 0.88 | 28 | LYS |
| 4 | 619 | 0.69 | 0.77 | 54 | empty |
| 5 | 192 | 0.52 | 0.78 | 29 | empty |
Interfaces
6 interfaces between chains.
- A–D · 1533 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1497 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 1477 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1061 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1026 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (nonstandard).
Compared structures
- 7KWP · Dihydrodipicolinate synthase (DHDPS) from C.jejuni with pyruvate bound in the active site… · the same entry in another collection · chain D against D, 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 7KWP · PDBe 7KWP · UniProt Q9PPB4
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