Research workbench
Crystal structure of IRAK4 kinase domain complexed with amppnp
Analyse Crystal structure of IRAK4 kinase domain complexed with amppnp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OID
- Type
- protein
- Length
- 1,076 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interleukin-1 receptor-associated kinase 4
- EC
- 2.7.11.1
- UniProt
- Q9NWZ3
- Ligands
- ANP
- Pockets
- 13 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1) | protein | 266 | 39% helix, 17% strand | Q9NWZ3 |
| B | Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1) | protein | 274 | 42% helix, 15% strand | Q9NWZ3 |
| C | Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1) | protein | 259 | 42% helix, 15% strand | Q9NWZ3 |
| D | Interleukin-1 receptor-associated kinase 4 (EC 2.7.11.1) | protein | 277 | 39% helix, 17% strand | Q9NWZ3 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 817 | 0.84 | 0.87 | 110 | empty |
| 2 | 347 | 0.80 | 0.90 | 44 | empty |
| 3 | 830 | 0.73 | 0.77 | 56 | empty |
| 4 | 763 | 0.71 | 0.77 | 53 | empty |
| 5 | 167 | 0.67 | 0.87 | 29 | ANP |
Interfaces
5 interfaces between chains.
- A–D · 644 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 596 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 556 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 500 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 351 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 11 modified (phosphorylation).
Compared structures
- 2OID · Crystal structure of IRAK4 kinase domain complexed with AMPPNP · the same entry in another collection · chain D against D, TM-score 1.00
- Q9NWZ3 · AlphaFold monomer V2.0 prediction for interleukin-1 receptor- associated kinase 4 (Q9NWZ3) · a predicted model of the same protein · chain C 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 Q9NWZ3
- Elsewhere: RCSB PDB 2OID · PDBe 2OID · UniProt Q9NWZ3
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