Research workbench
Sr protein kinase 1 (SRPK1) in complex with the rgg-box of HSV1 ICP27
Analyse Sr protein kinase 1 (SRPK1) in complex with the rgg-box of HSV1 ICP27 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FAD
- Type
- protein
- Length
- 1,462 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Srsf protein kinase 1; MRNA export factor
- EC
- 2.7.11.1
- UniProt
- Q96SB4, P36295
- Ligands
- PO4
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Srsf protein kinase 1 (EC 2.7.11.1) | protein | 356 | 42% helix, 16% strand | Q96SB4 |
| C | Srsf protein kinase 1 (EC 2.7.11.1) | protein | 359 | 42% helix, 16% strand | Q96SB4 |
| E | MRNA export factor | protein | 12 | 0% helix, 0% strand | P36295 |
| F | MRNA export factor | protein | 7 | 0% helix, 0% strand | P36295 |
| G, H | MRNA export factor | protein | 8 | 0% helix, 0% strand | P36295 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 5 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 951 | 0.81 | 0.83 | 102 | empty |
| 2 | 1051 | 0.79 | 0.80 | 98 | empty |
| 3 | 949 | 0.78 | 0.80 | 86 | empty |
| 4 | 882 | 0.76 | 0.80 | 92 | empty |
| 5 | 488 | 0.72 | 0.81 | 41 | empty |
Interfaces
9 interfaces between chains.
- B–C · 826 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 771 Ų buried · 6 hydrogen bonds · protein-protein
- B–H · 660 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 640 Ų buried · 13 hydrogen bonds · protein-protein
- C–G · 612 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6FAD · SR protein kinase 1 (SRPK1) in complex with the RGG-box of HSV1 ICP27 · the same entry in another collection · chain H against H, TM-score 1.00
- Q96SB4 · AlphaFold monomer V2.0 prediction for srsf protein kinase 1 (Q96SB4) · a predicted model of the same protein · chain A 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 Q96SB4
- Every structure of UniProt P36295
- Elsewhere: RCSB PDB 6FAD · PDBe 6FAD · UniProt Q96SB4 · UniProt P36295
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