Research workbench
Crystal structure of dihydrodipicolinate synthase (TM1521) from thermotoga maritima at 1.80 a resolution
Analyse Crystal structure of dihydrodipicolinate synthase (TM1521) from thermotoga… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1O5K
- Type
- protein
- Length
- 590 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-hydroxy-tetrahydrodipicolinate synthase
- EC
- 4.3.3.7
- UniProt
- Q9X1K9
- Ligands
- CA
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) | protein | 295 | 52% helix, 14% strand | Q9X1K9 |
Ligands and binding sites
- CA · Calcium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 531 | 0.73 | 0.81 | 57 | empty |
| 2 | 130 | 0.51 | 0.80 | 24 | empty |
| 3 | 110 | 0.45 | 0.79 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1462 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 1O5K · Crystal structure of Dihydrodipicolinate synthase (TM1521) from Thermotoga maritima at… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9X1K9 · AlphaFold monomer V2.0 prediction for 4-hydroxy- tetrahydrodipicolinate synthase (Q9X1K9) · 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 Q9X1K9
- Elsewhere: RCSB PDB 1O5K · PDBe 1O5K · UniProt Q9X1K9
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