MolNFT v1 · #179787 · protein
Dihydrodipicolinate synthase (dhdps) from C.JEJUNI, H59K mutant with pyruvate bound in the active site and L-histidine bound at the allosteric site
7KG2 · 4-hydroxy-tetrahydrodipicolinate synthase: “Dihydrodipicolinate synthase (dhdps) from C.JEJUNI, H59K mutant with pyruvate bound in the active site and…”. X-ray diffraction, 2 ligands (HIS, MG), 12 pockets (best druggability 0.73).…
- PDB
- 7KG2
- 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
- A0A2U0QMK8
- Ligands
- HIS, MG
- Pockets
- 12 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 48% 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 | 48% helix, 14% strand | A0A2U0QMK8 |
| F | 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) | protein | 297 | 48% helix, 14% strand | A0A2U0QMK8 |
Ligands and binding sites
- HIS · Histidine · ligand · 6 copies · chains A, C, B, D, E, F
- MG · Magnesium ion · metal · 14 copies · chains A, C, B, D, E, F
- EDO · 1,2-ethanediol · additive · 38 copies · chains A, B, C, D, E, F
- ACT · Acetate ion · additive · 15 copies · chains A, B, D, C, E, F
- PGE · Triethylene glycol · additive · 8 copies · chains A, B, C, D, E
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains D, C, E
- PG4 · Tetraethylene glycol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 366 | 0.73 | 0.84 | 47 | HIS |
| 2 | 355 | 0.72 | 0.84 | 48 | HIS |
| 3 | 364 | 0.71 | 0.83 | 48 | ACT, HIS |
| 4 | 560 | 0.68 | 0.78 | 60 | EDO, PGE |
| 5 | 200 | 0.52 | 0.77 | 24 | ACT |
Interfaces
6 interfaces between chains.
- A–C · 1501 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 1494 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 1490 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1013 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 981 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (nonstandard).
Compared structures
- 7KG2 · Dihydrodipicolinate synthase (DHDPS) from C.jejuni, H59K mutant with pyruvate bound in… · the same entry in another collection · 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 A0A2U0QMK8
- Elsewhere: RCSB PDB 7KG2 · PDBe 7KG2 · UniProt A0A2U0QMK8
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