MolNFT v1 · #91902 · protein
Crystal structure of human SERINE/THREONINE-protein kinase 32A (YANK1)
4FR4: “Crystal structure of human SERINE/THREONINE-protein kinase 32A (YANK1)”. X-ray diffraction, 1 ligand (STU), 20 pockets (best druggability 0.82). MolNFT v1 #91902 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4FR4
- Type
- protein
- Length
- 2,078 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase 32A
- EC
- 2.7.11.1
- UniProt
- Q8WU08
- Ligands
- STU
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 39% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase 32A (EC 2.7.11.1) | protein | 350 | 37% helix, 15% strand | Q8WU08 |
| B | SERINE/THREONINE-protein kinase 32A (EC 2.7.11.1) | protein | 350 | 36% helix, 15% strand | Q8WU08 |
| C | SERINE/THREONINE-protein kinase 32A (EC 2.7.11.1) | protein | 344 | 38% helix, 15% strand | Q8WU08 |
| D, F | SERINE/THREONINE-protein kinase 32A (EC 2.7.11.1) | protein | 346 | 41% helix, 15% strand | Q8WU08 |
| E | SERINE/THREONINE-protein kinase 32A (EC 2.7.11.1) | protein | 342 | 41% helix, 15% strand | Q8WU08 |
Ligands and binding sites
- STU · Staurosporine · ligand · 6 copies · chains A, B, C, D, E, F
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B, C, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 959 | 0.82 | 0.84 | 96 | STU |
| 2 | 736 | 0.77 | 0.81 | 83 | STU |
| 3 | 771 | 0.76 | 0.81 | 80 | STU |
| 4 | 697 | 0.75 | 0.81 | 76 | STU |
| 5 | 294 | 0.70 | 0.84 | 41 | STU, EDO |
Interfaces
8 interfaces between chains.
- A–F · 1192 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 1160 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 1053 Ų buried · 9 hydrogen bonds · protein-protein
- C–F · 1039 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 858 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4FR4 · Crystal structure of human serine/threonine-protein kinase 32A (YANK1) · the same entry in another collection · chain E against E, TM-score 1.00
- Q8WU08 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase 32A (Q8WU08) · a predicted model of the same protein · chain C against A, TM-score 0.95
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 Q8WU08
- Elsewhere: RCSB PDB 4FR4 · PDBe 4FR4 · UniProt Q8WU08
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