MolNFT v1 · #179991 · protein
Dihydrodipicolinate synthase (dhdps) from C.JEJUNI, H59N mutant with pyruvate bound in the active site and R,R-bislysine bound at the allosteric site
7KM1 · 4-hydroxy-tetrahydrodipicolinate synthase: “Dihydrodipicolinate synthase (dhdps) from C.JEJUNI, H59N mutant with pyruvate bound in the active site and…”. X-ray diffraction, 2 ligands (3VN, MG), 13 pockets (best druggability 0.76).…
- PDB
- 7KM1
- 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
- 3VN, MG
- Pockets
- 13 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) | protein | 296 | 46% helix, 14% strand | Q9PPB4 |
| F | 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) | protein | 297 | 46% helix, 14% strand | Q9PPB4 |
Ligands and binding sites
- 3VN · (2R,5R)-2,5-diamino-2,5-bis(4-aminobutyl)hexanedioic acid · ligand · 3 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 7 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 18 copies · chains A, B, C, D, E, F
- ACT · Acetate ion · additive · 9 copies · chains A, E, D, B, C, F
- PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains A, E, B, C, D
- PG4 · Tetraethylene glycol · additive · 5 copies · chains A, C, E, F
- PGE · Triethylene glycol · additive · 5 copies · chains B, C, D, E
- GOL · Glycerol · additive · 2 copies · chains E, 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 258 | 0.76 | 0.90 | 48 | 3VN |
| 2 | 249 | 0.75 | 0.89 | 51 | 3VN, EDO |
| 3 | 250 | 0.75 | 0.89 | 38 | 3VN |
| 4 | 599 | 0.68 | 0.77 | 62 | PEG, EDO |
| 5 | 198 | 0.55 | 0.79 | 24 | ACT |
Interfaces
6 interfaces between chains.
- A–B · 1516 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1515 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 1513 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1019 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 975 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (nonstandard).
Compared structures
- 7KM1 · Dihydrodipicolinate synthase (DHDPS) from C.jejuni, H59N 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 D 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 7KM1 · PDBe 7KM1 · UniProt Q9PPB4
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