Research workbench
Crystal structure of a naturally folded murine apoptosis inducing factor
Analyse Crystal structure of a naturally folded murine apoptosis inducing factor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GD3
- Type
- protein
- Length
- 1,888 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Apoptosis-inducing factor 1, mitochondrial
- UniProt
- Q9Z0X1
- Ligands
- FAD
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 6 distinct chains · 27% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Apoptosis-inducing factor 1, mitochondrial | protein | 463 | 30% helix, 29% strand | Q9Z0X1 |
| B | Apoptosis-inducing factor 1, mitochondrial | protein | 476 | 27% helix, 29% strand | Q9Z0X1 |
| C | Apoptosis-inducing factor 1, mitochondrial | protein | 467 | 27% helix, 29% strand | Q9Z0X1 |
| D | Apoptosis-inducing factor 1, mitochondrial | protein | 465 | 24% helix, 31% strand | Q9Z0X1 |
| E | Apoptosis-inducing factor 1, mitochondrial | protein | 8 | 0% helix, 25% strand | — |
| F | Apoptosis-inducing factor 1, mitochondrial | protein | 9 | 0% helix, 56% strand | — |
Ligands and binding sites
- FAD · Flavin-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
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1049 | 0.82 | 0.83 | 89 | FAD |
| 2 | 988 | 0.82 | 0.83 | 94 | FAD |
| 3 | 1110 | 0.81 | 0.82 | 95 | FAD |
| 4 | 1051 | 0.81 | 0.82 | 84 | FAD |
| 5 | 112 | 0.76 | 0.96 | 26 | empty |
Interfaces
7 interfaces between chains.
- B–C · 842 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 827 Ų buried · 14 hydrogen bonds · protein-protein
- A–F · 375 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 287 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 200 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3GD3 · Crystal structure of a naturally folded murine apoptosis inducing factor · the same entry in another collection · chain F against F, 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 A against A, TM-score 0.99
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 3GD3 · PDBe 3GD3 · UniProt Q9Z0X1
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