Research workbench
Flagellin derivative in complex with the nlr protein NAIP5
Analyse Flagellin derivative in complex with the nlr protein NAIP5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YUD
- Type
- protein
- Length
- 1,313 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Baculoviral iap repeat-containing protein 1E; Phase 2 FLAGELLIN,FLAGELLIN
- UniProt
- Q8CGT2, P52616, P06179
- Ligands
- ATP
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 2 distinct chains · 41% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Baculoviral iap repeat-containing protein 1E | protein | 1238 | 38% helix, 7% strand | Q8CGT2 |
| C | Phase 2 FLAGELLIN,FLAGELLIN | protein | 75 | 75% helix, 0% strand | P52616, P06179 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A
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 | 1139 | 0.85 | 0.86 | 129 | empty |
| 2 | 276 | 0.84 | 0.95 | 69 | empty |
| 3 | 194 | 0.81 | 0.95 | 41 | empty |
| 4 | 216 | 0.81 | 0.94 | 29 | empty |
| 5 | 161 | 0.80 | 0.96 | 50 | empty |
Interfaces
1 interface between chains.
- A–C · 3488 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 5YUD · Flagellin derivative in complex with the NLR protein NAIP5 · the same entry in another collection · chain A against A, TM-score 1.00
- P06179 · AlphaFold monomer V2.0 prediction for flagellin (P06179) · a predicted model of the same protein · chain C against A, TM-score 0.60
- P52616 · AlphaFold monomer V2.0 prediction for phase 2 flagellin (P52616) · a predicted model of the same protein · chain C against A, TM-score 0.56
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 Q8CGT2
- Every structure of UniProt P52616
- Every structure of UniProt P06179
- Elsewhere: RCSB PDB 5YUD · PDBe 5YUD · UniProt Q8CGT2 · UniProt P52616 · UniProt P06179
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