Research workbench
Catalytic domain of human PAK4 with rpkplvdp peptide
Analyse Catalytic domain of human PAK4 with rpkplvdp peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FIF
- Type
- protein
- Length
- 601 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase pak 4
- EC
- 2.7.11.1
- UniProt
- O96013
- Ligands
- ANP
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase pak 4 (EC 2.7.11.1) | protein | 294 | 43% helix, 18% strand | O96013 |
| B | SERINE/THREONINE-protein kinase pak 4 (EC 2.7.11.1) | protein | 293 | 43% helix, 18% strand | O96013 |
| C, D | SERINE/THREONINE-protein kinase pak 4 (EC 2.7.11.1) | protein | 7 | 0% helix, 14% strand | O96013 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 514 | 0.73 | 0.82 | 49 | ANP |
| 2 | 340 | 0.65 | 0.80 | 34 | ANP |
| 3 | 170 | 0.61 | 0.83 | 29 | empty |
| 4 | 115 | 0.42 | 0.77 | 28 | empty |
| 5 | 67 | 0.35 | 0.77 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 905 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 626 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 607 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 4FIF · Catalytic domain of human PAK4 with RPKPLVDP peptide · the same entry in another collection · chain A against A, TM-score 1.00
- O96013 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase pak 4 (O96013) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 O96013
- Elsewhere: RCSB PDB 4FIF · PDBe 4FIF · UniProt O96013
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