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The crystal structure of a dimeric mutant of dihydrodipicolinate synthase from E.COLI- dhdps-L197Y
Analyse The crystal structure of a dimeric mutant of dihydrodipicolinate synthase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OJP
- 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
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dihydrodipicolinate synthase (EC 4.2.1.52) | protein | 292 | 47% helix, 12% strand | P0A6L2 |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 414 | 0.72 | 0.83 | 69 | empty |
| 2 | 98 | 0.38 | 0.75 | 21 | empty |
| 3 | 73 | 0.34 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1359 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard, oxidation).
Compared structures
- 2OJP · The crystal structure of a dimeric mutant of Dihydrodipicolinate synthase from E.coli… · 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 0.99
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 2OJP · PDBe 2OJP · UniProt P0A6L2
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