Research workbench
R. rubrum transhydrogenase asymmetric complex (dI.NAD+)2(dIII.NADP+)1
Analyse R. rubrum transhydrogenase asymmetric complex (dI.NAD+)2(dIII.NADP+)1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1U28
- Type
- protein
- Length
- 911 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.3
- Source
- Rhodospirillum rubrum
- Molecule
- NAD(P) transhydrogenase subunit alpha part 1; NAD(P) transhydrogenase subunit beta
- EC
- 1.6.1.2
- UniProt
- Q60164, Q59765
- Ligands
- NAD, NAP
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · resolution 2.3 · 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 | 378 | 37% helix, 17% strand | Q60164 |
| B | NAD(P) transhydrogenase subunit alpha part 1 (EC 1.6.1.2) | protein | 359 | 37% helix, 19% strand | Q60164 |
| C | NAD(P) transhydrogenase subunit beta (EC 1.6.1.2) | protein | 174 | 40% helix, 18% strand | Q59765 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · chains B, C
- GOL · Glycerol · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1178 | 0.77 | 0.79 | 111 | NAD, GOL, NAP |
| 2 | 943 | 0.76 | 0.79 | 75 | NAD |
| 3 | 394 | 0.61 | 0.76 | 49 | empty |
| 4 | 283 | 0.51 | 0.74 | 44 | empty |
| 5 | 179 | 0.49 | 0.77 | 29 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1771 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 710 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 442 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1U28 · R. rubrum transhydrogenase asymmetric complex (DI.NAD+)2(DIII.NADP+)1 · 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 1U28 · PDBe 1U28 · UniProt Q60164 · UniProt Q59765
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