Research workbench
Crystal structure of the reduced, NAD-bound form of murine apoptosis inducing factor
Analyse Crystal structure of the reduced, NAD-bound form of murine apoptosis inducing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GD4
- Type
- protein
- Length
- 880 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Apoptosis-inducing factor 1, mitochondrial
- UniProt
- Q9Z0X1
- Ligands
- FAD, NAD
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Apoptosis-inducing factor 1, mitochondrial | protein | 445 | 27% helix, 31% strand | Q9Z0X1 |
| B | Apoptosis-inducing factor 1, mitochondrial | protein | 435 | 28% helix, 32% strand | Q9Z0X1 |
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
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 843 | 0.83 | 0.85 | 94 | FAD, NAD |
| 2 | 832 | 0.82 | 0.85 | 94 | FAD, NAD |
| 3 | 58 | 0.71 | 0.98 | 24 | empty |
| 4 | 202 | 0.45 | 0.73 | 32 | empty |
| 5 | 160 | 0.41 | 0.73 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 729 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 3GD4 · Crystal structure of the reduced, NAD-bound form of murine apoptosis inducing factor · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Z0X1 · AlphaFold monomer V2.0 prediction for apoptosis-inducing factor 1, mitochondrial (Q9Z0X1) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 Q9Z0X1
- Elsewhere: RCSB PDB 3GD4 · PDBe 3GD4 · UniProt Q9Z0X1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.