Research workbench
Crystal structure of L-threonine dehydrogenase from phytophthora infestans
Analyse Crystal structure of L-threonine dehydrogenase from phytophthora infestans in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JYG
- Type
- protein
- Length
- 1,836 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-threonine 3-dehydrogenase, putative
- UniProt
- D0N3N0
- Ligands
- NAD
- Pockets
- 13 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | L-threonine 3-dehydrogenase, putative | protein | 306 | 47% helix, 18% strand | D0N3N0 |
| D, F | L-threonine 3-dehydrogenase, putative | protein | 307 | 46% helix, 18% strand | D0N3N0 |
| E | L-threonine 3-dehydrogenase, putative | protein | 304 | 46% helix, 17% strand | D0N3N0 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 6 copies · chains A, B, C, D, E, F
- FLC · Citrate anion · additive · 7 copies · chains A, B, C, D, E, F
- PE8 · 3,6,9,12,15,18,21-heptaoxatricosane-1,23-diol · additive · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 453 | 0.76 | 0.84 | 47 | FLC, NAD |
| 2 | 476 | 0.76 | 0.84 | 46 | FLC, NAD |
| 3 | 531 | 0.76 | 0.83 | 53 | FLC, NAD |
| 4 | 421 | 0.75 | 0.84 | 48 | FLC, NAD |
| 5 | 546 | 0.75 | 0.82 | 54 | FLC, NAD |
Interfaces
5 interfaces between chains.
- D–F · 1340 Ų buried · 15 hydrogen bonds · protein-protein
- C–E · 1292 Ų buried · 21 hydrogen bonds · protein-protein
- B–F · 302 Ų buried · 2 hydrogen bonds · protein-protein
- A–E · 301 Ų buried · 2 hydrogen bonds · protein-protein
- B–E · 75 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6JYG · Crystal Structure of L-threonine dehydrogenase from Phytophthora infestans · 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 D0N3N0
- Elsewhere: RCSB PDB 6JYG · PDBe 6JYG · UniProt D0N3N0
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