MolNFT v2 · #16018 · protein
R. rubrum transhydrogenase (dI.Q132N)2(dIII)1 asymmetric complex
1NM5 · NAD(P) transhydrogenase subunit alpha part 1: “R. rubrum transhydrogenase (dI.Q132N)2(dIII)1 asymmetric complex”. X-ray diffraction at 2.4, 2 ligands (NAD, NAP), 10 pockets (best druggability 0.78). MolNFT v2 #16018 on GenesisL1: 3D…
- PDB
- 1NM5
- Type
- protein
- Length
- 892 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.4
- 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
- 10 · best druggability 0.78
Structure
x-ray diffraction · resolution 2.4 · 3 distinct chains · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD(P) transhydrogenase subunit alpha part 1 (EC 1.6.1.2) | protein | 360 | 38% helix, 18% strand | Q60164 |
| B | NAD(P) transhydrogenase subunit alpha part 1 (EC 1.6.1.2) | protein | 358 | 37% helix, 21% strand | Q60164 |
| C | NAD(P) transhydrogenase subunit beta (EC 1.6.1.2) | protein | 174 | 39% helix, 19% 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 · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1133 | 0.78 | 0.80 | 103 | NAD, GOL, NAP |
| 2 | 847 | 0.75 | 0.79 | 68 | NAD |
| 3 | 324 | 0.58 | 0.77 | 54 | empty |
| 4 | 167 | 0.44 | 0.75 | 30 | empty |
| 5 | 157 | 0.43 | 0.75 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1794 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 747 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 427 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1NM5 · R. rubrum transhydrogenase (DI.Q132N)2(DIII)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 1NM5 · PDBe 1NM5 · UniProt Q60164 · UniProt Q59765
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