Research workbench
Dihydrodipicolinate synthase mutant - K161A - with the substrate pyruvate bound in the active site.
Analyse Dihydrodipicolinate synthase mutant - K161A - with the substrate pyruvate bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3I7S
- Type
- protein
- Length
- 584 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrodipicolinate synthase
- EC
- 4.2.1.52
- UniProt
- P0A6L2
- Ligands
- PYR, K, PO4
- Pockets
- 2 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dihydrodipicolinate synthase (EC 4.2.1.52) | protein | 292 | 47% helix, 13% strand | P0A6L2 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 6 copies · chains A, B
- PO4 · Phosphate ion · ion · 3 copies · chains A, B
- GOL · Glycerol · additive · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 629 | 0.79 | 0.84 | 77 | GOL, K, PYR |
| 2 | 111 | 0.58 | 0.85 | 24 | PYR |
Interfaces
1 interface between chains.
- A–B · 1360 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3I7S · Dihydrodipicolinate synthase mutant - K161A - with the substrate pyruvate bound in the… · the same entry in another collection · chain A against A, TM-score 1.00
- P0A6L2 · AlphaFold monomer V2.0 prediction for 4-hydroxy- tetrahydrodipicolinate synthase (P0A6L2) · 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 P0A6L2
- Elsewhere: RCSB PDB 3I7S · PDBe 3I7S · UniProt P0A6L2
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