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Three-dimensional structure of L-threonine 3-dehydrogenase from trypanosoma brucei bound to NADH and L-threonine refined to 1.72 ångströms
Analyse Three-dimensional structure of L-threonine 3-dehydrogenase from trypanosoma… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5K4W
- Type
- protein
- Length
- 641 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-threonine 3-dehydrogenase
- EC
- 1.1.1.103
- UniProt
- Q7YW97
- Ligands
- NAI, THR, NA
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-threonine 3-dehydrogenase (EC 1.1.1.103) | protein | 320 | 47% helix, 15% strand | Q7YW97 |
| C | L-threonine 3-dehydrogenase (EC 1.1.1.103) | protein | 321 | 47% helix, 15% strand | Q7YW97 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 2 copies · chains A, C
- THR · Threonine · ligand · 2 copies · chains A, C
- NA · Sodium ion · metal · 2 copies · chains A, C
- GOL · Glycerol · additive · 3 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 368 | 0.76 | 0.86 | 48 | NAI, THR |
| 2 | 362 | 0.76 | 0.86 | 45 | NAI, THR |
| 3 | 284 | 0.73 | 0.87 | 42 | empty |
| 4 | 56 | 0.33 | 0.77 | 12 | empty |
| 5 | 50 | 0.30 | 0.76 | 12 | GOL |
Interfaces
1 interface between chains.
- A–C · 1314 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5K4W · Three-dimensional structure of L-threonine 3-dehydrogenase from Trypanosoma brucei bound… · the same entry in another collection · 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 Q7YW97
- Elsewhere: RCSB PDB 5K4W · PDBe 5K4W · UniProt Q7YW97
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