Research workbench
Structure of ovine transhydrogenase in the presence of NADP+ in a "double face-down" conformation
Analyse Structure of ovine transhydrogenase in the presence of NADP+ in a "double… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QTI
- Type
- protein
- Length
- 2,076 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nicotinamide nucleotide transhydrogenase
- UniProt
- W5PFI3
- Ligands
- PC1, D12, NAP, NAD
- Pockets
- 20 · best druggability 0.77
Structure
electron microscopy · 1 distinct chain · 49% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nicotinamide nucleotide transhydrogenase | protein | 1038 | 49% helix, 8% strand | W5PFI3 |
Ligands and binding sites
- PC1 · 1,2-diacyl-sn-glycero-3-phosphocholine · ligand · 12 copies · chains A, B
- D12 · Dodecane · ligand · 3 copies · chains A, B
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1044 | 0.77 | 0.79 | 90 | NAD |
| 2 | 835 | 0.76 | 0.80 | 78 | NAD |
| 3 | 657 | 0.76 | 0.81 | 80 | NAP |
| 4 | 539 | 0.74 | 0.82 | 62 | NAP |
| 5 | 1037 | 0.71 | 0.75 | 110 | empty |
Interfaces
1 interface between chains.
- A–B · 4442 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 6QTI · Structure of ovine transhydrogenase in the presence of NADP+ in a "double face-down"… · the same entry in another collection · chain A against A, TM-score 1.00
- W5PFI3 · AlphaFold monomer V2.0 prediction for NAD(P) transhydrogenase, mitochondrial (W5PFI3) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 W5PFI3
- Elsewhere: RCSB PDB 6QTI · PDBe 6QTI · UniProt W5PFI3
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