Research workbench
Crystal structure of human RIPK3 complexed with GSK'843
Analyse Crystal structure of human RIPK3 complexed with GSK'843 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MX3
- Type
- protein
- Length
- 1,126 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Receptor-interacting SERINE/THREONINE-protein kinase 3
- EC
- 2.7.11.1
- UniProt
- Q9Y572
- Ligands
- ZOV
- Pockets
- 14 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Receptor-interacting SERINE/THREONINE-protein kinase 3 (EC 2.7.11.1) | protein | 292 | 41% helix, 15% strand | Q9Y572 |
| B | Receptor-interacting SERINE/THREONINE-protein kinase 3 (EC 2.7.11.1) | protein | 269 | 39% helix, 14% strand | Q9Y572 |
| C | Receptor-interacting SERINE/THREONINE-protein kinase 3 (EC 2.7.11.1) | protein | 285 | 37% helix, 12% strand | Q9Y572 |
| D | Receptor-interacting SERINE/THREONINE-protein kinase 3 (EC 2.7.11.1) | protein | 280 | 37% helix, 17% strand | Q9Y572 |
Ligands and binding sites
- ZOV · 3-(1,3-benzothiazol-5-yl)-7-(1,3-dimethyl-1H-pyrazol-5-yl)thieno[3,2-c]pyridin-4-amine · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 389 | 0.70 | 0.82 | 50 | ZOV |
| 2 | 372 | 0.67 | 0.80 | 54 | ZOV |
| 3 | 256 | 0.65 | 0.82 | 32 | empty |
| 4 | 367 | 0.64 | 0.79 | 49 | ZOV |
| 5 | 305 | 0.62 | 0.79 | 41 | ZOV |
Interfaces
4 interfaces between chains.
- A–C · 747 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 403 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 66 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 38 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7MX3 · Crystal structure of human RIPK3 complexed with GSK'843 · the same entry in another collection · chain D against D, TM-score 1.00
- Q9Y572 · AlphaFold monomer V2.0 prediction for receptor-interacting SERINE/THREONINE-protein… · 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 Q9Y572
- Elsewhere: RCSB PDB 7MX3 · PDBe 7MX3 · UniProt Q9Y572
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