Research workbench
Crystal structure analysis of the diii component of transhydrogenase with a thio-nicotinamide nucleotide analogue
Analyse Crystal structure analysis of the diii component of transhydrogenase with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PT9
- Type
- protein
- Length
- 364 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD(P) transhydrogenase, mitochondrial
- EC
- 1.6.1.2
- UniProt
- Q13423
- Ligands
- TAP, SO4
- Pockets
- 3 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | NAD(P) transhydrogenase, mitochondrial (EC 1.6.1.2) | protein | 182 | 41% helix, 16% strand | Q13423 |
Ligands and binding sites
- TAP · 7-thionicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 248 | 0.58 | 0.79 | 32 | TAP, GOL |
| 2 | 221 | 0.56 | 0.79 | 33 | TAP, GOL |
| 3 | 244 | 0.51 | 0.75 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 58 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1PT9 · Crystal Structure Analysis of the DIII Component of Transhydrogenase with a… · the same entry in another collection · chain A against A, TM-score 1.00
- Q13423 · AlphaFold monomer V2.0 prediction for NAD(P) transhydrogenase, mitochondrial (Q13423) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q13423
- Elsewhere: RCSB PDB 1PT9 · PDBe 1PT9 · UniProt Q13423
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