Research workbench
Crystal structure of E. COLI dihydrodipicolinate synthase with pyruvate and succinic semi-aldehyde bound in active site
Analyse Crystal structure of E. COLI dihydrodipicolinate synthase with pyruvate and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EOU
- 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
- K
- Pockets
- 3 · best druggability 0.76
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
- K · Potassium ion · metal · 4 copies · chains A, B
- 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 | 430 | 0.76 | 0.85 | 59 | GOL |
| 2 | 96 | 0.36 | 0.75 | 20 | empty |
| 3 | 84 | 0.34 | 0.75 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1360 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 4EOU · Crystal structure of E. coli dihydrodipicolinate synthase with pyruvate and succinic… · 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 B 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 4EOU · PDBe 4EOU · UniProt P0A6L2
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