Research workbench
Kinetic, spectral and structural characterization of the slow binding inhibitor acetopyruvate with dihydrodipicolinate synthase from escherichia COLI.
Analyse Kinetic, spectral and structural characterization of the slow binding inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5T26
- Type
- protein
- Length
- 587 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
- B7M7I1
- Ligands
- NA
- Pockets
- 5 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) | protein | 293 | 46% helix, 13% strand | B7M7I1 |
| B | 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) | protein | 294 | 48% helix, 13% strand | B7M7I1 |
Ligands and binding sites
- NA · Sodium ion · metal · 7 copies · chains A, B
- TLA · L(+)-tartaric acid · additive · chains B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 178 | 0.56 | 0.80 | 31 | empty |
| 2 | 161 | 0.55 | 0.81 | 31 | GOL |
| 3 | 149 | 0.51 | 0.79 | 29 | empty |
| 4 | 84 | 0.38 | 0.77 | 19 | empty |
| 5 | 55 | 0.33 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 542 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 5T26 · Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor… · the same entry in another collection · chain A against A, TM-score 1.00
- B7M7I1 · AlphaFold monomer V2.0 prediction for 4-hydroxy- tetrahydrodipicolinate synthase (B7M7I1) · 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 B7M7I1
- Elsewhere: RCSB PDB 5T26 · PDBe 5T26 · UniProt B7M7I1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.