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The X-ray structure of nicotinamide nucleotide transhydrogenase from rhodospirillum rubrum complexed with NAD+
Analyse The X-ray structure of nicotinamide nucleotide transhydrogenase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1F8G
- Type
- protein
- Length
- 1,515 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nicotinamide nucleotide transhydrogenase
- EC
- 1.6.1.1
- UniProt
- Q60164
- Ligands
- NAD
- Pockets
- 15 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nicotinamide nucleotide transhydrogenase (EC 1.6.1.1) | protein | 382 | 38% helix, 19% strand | Q60164 |
| B | Nicotinamide nucleotide transhydrogenase (EC 1.6.1.1) | protein | 381 | 38% helix, 19% strand | Q60164 |
| C | Nicotinamide nucleotide transhydrogenase (EC 1.6.1.1) | protein | 375 | 39% helix, 19% strand | Q60164 |
| D | Nicotinamide nucleotide transhydrogenase (EC 1.6.1.1) | protein | 377 | 38% helix, 18% strand | Q60164 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 996 | 0.79 | 0.81 | 86 | NAD |
| 2 | 1134 | 0.78 | 0.80 | 105 | NAD |
| 3 | 811 | 0.78 | 0.81 | 67 | NAD |
| 4 | 823 | 0.77 | 0.81 | 71 | NAD |
| 5 | 290 | 0.56 | 0.76 | 39 | empty |
Interfaces
4 interfaces between chains.
- A–C · 1819 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 1782 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 423 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 263 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 59 modified (engineered).
Compared structures
- 1F8G · The X-ray structure of nicotinamide nucleotide transhydrogenase from rhodospirillum… · 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
- Elsewhere: RCSB PDB 1F8G · PDBe 1F8G · UniProt Q60164
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