Research workbench
Crystal structure of amppnp-bound human PRPF4B kinase domain
Analyse Crystal structure of amppnp-bound human PRPF4B kinase domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IIR
- Type
- protein
- Length
- 654 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase PRP4 homolog
- EC
- 2.7.11.1
- UniProt
- Q13523
- Ligands
- ANP, MG, SO4
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase PRP4 homolog (EC 2.7.11.1) | protein | 326 | 39% helix, 19% strand | Q13523 |
| B | SERINE/THREONINE-protein kinase PRP4 homolog (EC 2.7.11.1) | protein | 328 | 39% helix, 19% strand | Q13523 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 269 | 0.65 | 0.82 | 33 | ANP |
| 2 | 277 | 0.63 | 0.80 | 32 | ANP, MG |
| 3 | 184 | 0.44 | 0.74 | 29 | empty |
| 4 | 89 | 0.37 | 0.76 | 16 | empty |
| 5 | 91 | 0.34 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 566 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 4IIR · Crystal Structure of AMPPNP-bound Human PRPF4B kinase domain · the same entry in another collection · chain A against A, TM-score 1.00
- Q13523 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase PRP4 homolog… · a predicted model of the same protein · chain B 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 Q13523
- Elsewhere: RCSB PDB 4IIR · PDBe 4IIR · UniProt Q13523
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