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Dihydrodipicolinate synthase (dhdps) from C.JEJUNI, H59K mutant with pyruvate bound in the active site
Analyse Dihydrodipicolinate synthase (dhdps) from C.JEJUNI, H59K mutant with pyruvate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KEL
- Type
- protein
- Length
- 3,547 residues
- Chains
- 12
- 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
- MG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E | 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) | protein | 295 | 48% helix, 14% strand | A0A2U0QMK8 |
| B, C, F, G, H, I, K, L | 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) | protein | 296 | 47% helix, 14% strand | A0A2U0QMK8 |
| J | 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) | protein | 294 | 48% helix, 14% strand | A0A2U0QMK8 |
Ligands and binding sites
- MG · Magnesium ion · metal · 6 copies · chains A, C, D, E
- EDO · 1,2-ethanediol · additive · 56 copies · chains A, B, C, F, H, D, G, E, K, J, I, L
- ACT · Acetate ion · additive · 19 copies · chains A, B, F, C, E, H, I, L, J
- PGE · Triethylene glycol · additive · 10 copies · chains A, C, D, E, F, I, J, K, L
- PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains F, G, H, J, L, I
- GOL · Glycerol · additive · 3 copies · chains G, I, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 874 | 0.82 | 0.84 | 107 | EDO |
| 2 | 334 | 0.75 | 0.86 | 54 | ACT, EDO |
| 3 | 395 | 0.73 | 0.84 | 63 | EDO |
| 4 | 431 | 0.73 | 0.83 | 63 | EDO, ACT |
| 5 | 339 | 0.73 | 0.85 | 52 | EDO |
Interfaces
18 interfaces between chains.
- D–G · 1473 Ų buried · 18 hydrogen bonds · protein-protein
- H–J · 1472 Ų buried · 15 hydrogen bonds · protein-protein
- I–L · 1466 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1457 Ų buried · 14 hydrogen bonds · protein-protein
- C–F · 1433 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (nonstandard).
Compared structures
- 7KEL · 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 7KEL · PDBe 7KEL · UniProt A0A2U0QMK8
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