Research workbench
Partial consensus L-threonine 3-dehydrogenase (E-change)
Analyse Partial consensus L-threonine 3-dehydrogenase (E-change) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EPS
- Type
- protein
- Length
- 1,231 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-threonine 3-dehydrogenase
- Ligands
- NAD, THR
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | L-threonine 3-dehydrogenase | protein | 310 | 46% helix, 15% strand | — |
| B | L-threonine 3-dehydrogenase | protein | 306 | 46% helix, 15% strand | — |
| D | L-threonine 3-dehydrogenase | protein | 305 | 47% helix, 15% strand | — |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- THR · Threonine · ligand · 4 copies · chains A, B, C, D
- PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 891 | 0.81 | 0.83 | 115 | empty |
| 2 | 305 | 0.75 | 0.87 | 42 | NAD, THR |
| 3 | 287 | 0.74 | 0.87 | 43 | NAD, THR |
| 4 | 289 | 0.74 | 0.87 | 42 | NAD, THR |
| 5 | 321 | 0.74 | 0.86 | 42 | NAD, THR |
Interfaces
5 interfaces between chains.
- C–D · 1018 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1001 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 450 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 100 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 98 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7EPS · Partial Consensus L-threonine 3-dehydrogenase (E-change) · 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
- Elsewhere: RCSB PDB 7EPS · PDBe 7EPS
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