Research workbench
Cryo-EM structure of the pyd filament of AIM2
Analyse Cryo-EM structure of the pyd filament of AIM2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MB2
- Type
- protein
- Length
- 4,785 residues
- Chains
- 30
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interferon-inducible protein AIM2; Green fluorescent protein
- UniProt
- O14862, P42212
- Ligands
- CRO
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 2 distinct chains · 26% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O | Interferon-inducible protein AIM2 | protein | 94 | 65% helix, 0% strand | O14862 |
| a, b, c, d, e, f, g, h, i, j, k, l, m, n, o | Green fluorescent protein | protein | 225 | 10% helix, 52% strand | P42212 |
Ligands and binding sites
- CRO · {2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · 15 copies · chains a, b, c, d, e, f, g, h, i, j, k, l, m, n, o
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1078 | 0.84 | 0.85 | 127 | empty |
| 2 | 1141 | 0.83 | 0.84 | 144 | empty |
| 3 | 119 | 0.80 | 0.98 | 28 | CRO |
| 4 | 117 | 0.79 | 0.97 | 25 | CRO |
| 5 | 110 | 0.79 | 0.98 | 28 | CRO |
Interfaces
54 interfaces between chains.
- L–O · 249 Ų buried · 1 hydrogen bond · protein-protein
- C–F · 248 Ų buried · 1 hydrogen bond · protein-protein
- J–M · 246 Ų buried · 1 hydrogen bond · protein-protein
- K–N · 239 Ų buried · 1 hydrogen bond · protein-protein
- G–J · 238 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 60 modified, 30 cofactor (engineered, chromophore).
Compared structures
- 6MB2 · Cryo-EM structure of the PYD filament of AIM2 · the same entry in another collection · chain J against J, 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 O14862
- Every structure of UniProt P42212
- Elsewhere: RCSB PDB 6MB2 · PDBe 6MB2 · UniProt O14862 · UniProt P42212
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