MolNFT v1 · #95796 · protein
Crystal structure of thermus thermophilus transhydrogenase heterotrimeric complex of the ALPHA1 subunit dimer with the NADP binding domain (domain III) of the beta subunit
4J16 · NAD/NADP transhydrogenase alpha subunit 1: “Crystal structure of thermus thermophilus transhydrogenase heterotrimeric complex of the ALPHA1 subunit dimer…”. X-ray diffraction, 3 ligands (NAD, NAP, CL), 7 pockets (best druggability…
- PDB
- 4J16
- Type
- protein
- Length
- 918 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD/NADP transhydrogenase alpha subunit 1; NAD(P) transhydrogenase subunit beta
- EC
- 1.6.1.2
- UniProt
- Q72GR8, Q72GS0
- Ligands
- NAD, NAP, CL
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD/NADP transhydrogenase alpha subunit 1 (EC 1.6.1.2) | protein | 372 | 38% helix, 19% strand | Q72GR8 |
| B | NAD/NADP transhydrogenase alpha subunit 1 (EC 1.6.1.2) | protein | 369 | 37% helix, 19% strand | Q72GR8 |
| C | NAD(P) transhydrogenase subunit beta (EC 1.6.1.2) | protein | 177 | 43% helix, 18% strand | Q72GS0 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · chains A, C
- CL · Chloride ion · ion · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B, C
- PGE · Triethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1057 | 0.82 | 0.83 | 121 | NAD, NAP |
| 2 | 932 | 0.76 | 0.79 | 69 | NAD, PGE |
| 3 | 173 | 0.47 | 0.76 | 26 | GOL |
| 4 | 184 | 0.46 | 0.75 | 30 | empty |
| 5 | 125 | 0.40 | 0.75 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1945 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 725 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 437 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4J16 · Crystal structure of Thermus thermophilus transhydrogenase heterotrimeric complex of the… · 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 Q72GR8
- Every structure of UniProt Q72GS0
- Elsewhere: RCSB PDB 4J16 · PDBe 4J16 · UniProt Q72GR8 · UniProt Q72GS0
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