MolNFT v1 · #37133 · protein
Structure of transhydrogenase (DI.S138A.NADH)2(DIII.NADPH)1 asymmetric complex
2FRD · NAD(P) transhydrogenase subunit alpha part 1: “Structure of transhydrogenase (DI.S138A.NADH)2(DIII.NADPH)1 asymmetric complex”. X-ray diffraction, 2 ligands (NAI, NDP), 8 pockets (best druggability 0.77). MolNFT v1 #37133 on…
- PDB
- 2FRD
- Type
- protein
- Length
- 896 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD(P) transhydrogenase subunit alpha part 1; NAD(P) transhydrogenase subunit beta
- EC
- 1.6.1.2
- UniProt
- Q60164, Q59765
- Ligands
- NAI, NDP
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD(P) transhydrogenase subunit alpha part 1 (EC 1.6.1.2) | protein | 360 | 39% helix, 18% strand | Q60164 |
| B | NAD(P) transhydrogenase subunit alpha part 1 (EC 1.6.1.2) | protein | 362 | 36% helix, 20% strand | Q60164 |
| C | NAD(P) transhydrogenase subunit beta (EC 1.6.1.2) | protein | 174 | 37% helix, 17% strand | Q59765 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 2 copies · chains A, B, C
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1153 | 0.77 | 0.79 | 114 | NAI, NDP |
| 2 | 894 | 0.76 | 0.79 | 72 | NAI |
| 3 | 220 | 0.49 | 0.75 | 33 | empty |
| 4 | 191 | 0.48 | 0.76 | 28 | empty |
| 5 | 152 | 0.44 | 0.75 | 26 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1805 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 717 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 438 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2FRD · Structure of Transhydrogenase (dI.S138A.NADH)2(dIII.NADPH)1 asymmetric complex · 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
- Every structure of UniProt Q60164
- Every structure of UniProt Q59765
- Elsewhere: RCSB PDB 2FRD · PDBe 2FRD · UniProt Q60164 · UniProt Q59765
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