Research workbench
Structure of the NDI1 protein from saccharomyces cerevisiae in complex with NAD+
Analyse Structure of the NDI1 protein from saccharomyces cerevisiae in complex with NAD+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GAP
- Type
- protein
- Length
- 926 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rotenone-insensitive NADH-ubiquinone oxidoreductase
- EC
- 1.6.5.9
- UniProt
- P32340
- Ligands
- FAD, NAD
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Rotenone-insensitive NADH-ubiquinone oxidoreductase (EC 1.6.5.9) | protein | 463 | 36% helix, 26% strand | P32340 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 930 | 0.81 | 0.83 | 99 | FAD, NAD |
| 2 | 934 | 0.80 | 0.82 | 91 | FAD, NAD |
| 3 | 374 | 0.80 | 0.89 | 45 | empty |
| 4 | 526 | 0.77 | 0.84 | 55 | empty |
| 5 | 90 | 0.74 | 0.97 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 2019 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 4GAP · Structure of the Ndi1 protein from Saccharomyces cerevisiae in complex with NAD+ · the same entry in another collection · chain A against A, TM-score 1.00
- P32340 · AlphaFold monomer V2.0 prediction for rotenone-insensitive NADH- ubiquinone… · a predicted model of the same protein · 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 P32340
- Elsewhere: RCSB PDB 4GAP · PDBe 4GAP · UniProt P32340
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