MolNFT v1 · #75499 · protein
PDZ domain from human microtubule-associated SERINE/THREONINE-protein kinase 1
3PS4: “PDZ domain from human microtubule-associated SERINE/THREONINE-protein kinase 1”. X-ray diffraction, 3 pockets (best druggability 0.74). MolNFT v1 #75499 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3PS4
- Type
- protein
- Length
- 388 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Microtubule-associated SERINE/THREONINE-protein kinase 1
- EC
- 2.7.11.1
- UniProt
- Q9Y2H9
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Microtubule-associated SERINE/THREONINE-protein kinase 1 (EC 2.7.11.1) | protein | 96 | 16% helix, 42% strand | Q9Y2H9 |
| B | Microtubule-associated SERINE/THREONINE-protein kinase 1 (EC 2.7.11.1) | protein | 97 | 15% helix, 41% strand | Q9Y2H9 |
| D | Microtubule-associated SERINE/THREONINE-protein kinase 1 (EC 2.7.11.1) | protein | 99 | 15% helix, 38% strand | Q9Y2H9 |
Ligands and binding sites
- IMD · Imidazole · additive · 3 copies · chains B, C, A, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1148 | 0.74 | 0.77 | 109 | EDO |
| 2 | 63 | 0.51 | 0.86 | 18 | empty |
| 3 | 70 | 0.41 | 0.80 | 17 | empty |
Interfaces
6 interfaces between chains.
- A–D · 1913 Ų buried · 35 hydrogen bonds · protein-protein
- B–C · 1618 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 375 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 52 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 45 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3PS4 · PDZ domain from Human microtubule-associated serine/threonine-protein kinase 1 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y2H9 · AlphaFold monomer V2.0 prediction for microtubule-associated SERINE/THREONINE-protein… · a predicted model of the same protein · chain B against A, TM-score 0.88
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 Q9Y2H9
- Elsewhere: RCSB PDB 3PS4 · PDBe 3PS4 · UniProt Q9Y2H9
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