Research workbench
Mouse tdh mutant R180K with NAD+ bound
Analyse Mouse tdh mutant R180K with NAD+ bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YRB
- Type
- protein
- Length
- 1,333 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-threonine 3-dehydrogenase, mitochondrial
- EC
- 1.1.1.103
- UniProt
- Q8K3F7
- Ligands
- NAD
- Pockets
- 9 · best druggability 0.63
Structure
x-ray diffraction · 6 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-threonine 3-dehydrogenase, mitochondrial (EC 1.1.1.103) | protein | 206 | 50% helix, 16% strand | Q8K3F7 |
| B | L-threonine 3-dehydrogenase, mitochondrial (EC 1.1.1.103) | protein | 215 | 50% helix, 18% strand | Q8K3F7 |
| C | L-threonine 3-dehydrogenase, mitochondrial (EC 1.1.1.103) | protein | 249 | 45% helix, 17% strand | Q8K3F7 |
| D | L-threonine 3-dehydrogenase, mitochondrial (EC 1.1.1.103) | protein | 232 | 49% helix, 18% strand | Q8K3F7 |
| E | L-threonine 3-dehydrogenase, mitochondrial (EC 1.1.1.103) | protein | 223 | 47% helix, 16% strand | Q8K3F7 |
| F | L-threonine 3-dehydrogenase, mitochondrial (EC 1.1.1.103) | protein | 208 | 48% helix, 15% strand | Q8K3F7 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 308 | 0.63 | 0.79 | 36 | NAD |
| 2 | 281 | 0.61 | 0.79 | 30 | NAD |
| 3 | 256 | 0.60 | 0.79 | 33 | NAD |
| 4 | 288 | 0.60 | 0.78 | 32 | NAD |
| 5 | 311 | 0.60 | 0.78 | 31 | NAD |
Interfaces
7 interfaces between chains.
- C–D · 1208 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 1093 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1038 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 553 Ų buried · 6 hydrogen bonds · protein-protein
- B–F · 547 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
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 Q8K3F7
- Elsewhere: RCSB PDB 4YRB · PDBe 4YRB · UniProt Q8K3F7
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