Research workbench
Gale-like L-threonine dehydrogenase from cupriavidus necator (holo form)
Analyse Gale-like L-threonine dehydrogenase from cupriavidus necator (holo form) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WMX
- Type
- protein
- Length
- 1,230 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD dependent EPIMERASE/DEHYDRATASE
- EC
- 1.-.-.-
- UniProt
- Q0K312
- Ligands
- NAD, THR
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD dependent EPIMERASE/DEHYDRATASE (EC 1.-.-.-) | protein | 310 | 45% helix, 15% strand | Q0K312 |
| B, C | NAD dependent EPIMERASE/DEHYDRATASE (EC 1.-.-.-) | protein | 308 | 45% helix, 15% strand | Q0K312 |
| D | NAD dependent EPIMERASE/DEHYDRATASE (EC 1.-.-.-) | protein | 304 | 44% helix, 16% strand | Q0K312 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- THR · Threonine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 929 | 0.79 | 0.81 | 86 | NAD, THR |
| 2 | 879 | 0.79 | 0.82 | 88 | NAD, THR |
| 3 | 300 | 0.75 | 0.87 | 45 | NAD |
| 4 | 364 | 0.71 | 0.83 | 43 | NAD |
| 5 | 249 | 0.49 | 0.74 | 32 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1149 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 1107 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 828 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3WMX · GalE-like L-Threonine dehydrogenase from Cupriavidus necator (holo form) · the same entry in another collection · chain B against B, 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 Q0K312
- Elsewhere: RCSB PDB 3WMX · PDBe 3WMX · UniProt Q0K312
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