MolNFT v1 · #134373 · protein
Kinetic, spectral and structural characterization of the slow binding inhibitor acetopyruvate with dihydrodipicolinate synthase from escherichia COLI.
5T26 · 4-hydroxy-tetrahydrodipicolinate synthase: “Kinetic, spectral and structural characterization of the slow binding inhibitor acetopyruvate with…”. X-ray diffraction, 1 ligand (NA), 5 pockets (best druggability 0.56). MolNFT v1…
- 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.