Research workbench
ATP-competitive partial antagonists-'PAIR'S-rheostatically modulate IRE1ALPHA'S kinase helix-alphac to segregate its RNase-mediated biological outputs
Analyse ATP-competitive partial antagonists-'PAIR'S-rheostatically modulate IRE1ALPHA'S… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BMK
- Type
- protein
- Length
- 798 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein KINASE/ENDORIBONUCLEASE IRE1
- EC
- 2.7.11.1, 3.1.26.-
- UniProt
- O75460
- Ligands
- U4N
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein KINASE/ENDORIBONUCLEASE IRE1 (EC 2.7.11.1, 3.1.26.-) | protein | 406 | 45% helix, 14% strand | O75460 |
| B | SERINE/THREONINE-protein KINASE/ENDORIBONUCLEASE IRE1 (EC 2.7.11.1, 3.1.26.-) | protein | 392 | 45% helix, 15% strand | O75460 |
Ligands and binding sites
- U4N · 2,2,2-tris(fluoranyl)-~{N}-[4-[3-[2-[[(3~{S})-piperidin-3-yl]amino]pyrimidin-4-yl]pyridin-2-yl]oxynaphthalen-1-yl]ethanesulfonamide · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 19 copies · chains A, B
- GOL · Glycerol · additive · 10 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B
- PGE · Triethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 867 | 0.77 | 0.80 | 62 | EDO, GOL |
| 2 | 410 | 0.72 | 0.83 | 40 | U4N |
| 3 | 359 | 0.71 | 0.83 | 40 | U4N |
| 4 | 778 | 0.70 | 0.77 | 64 | EDO, PEG |
| 5 | 75 | 0.46 | 0.82 | 17 | GOL, PEG |
Interfaces
1 interface between chains.
- A–B · 1367 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 7BMK · ATP-Competitive Partial Antagonists-'PAIR's-Rheostatically Modulate IRE1alpha's Kinase… · the same entry in another collection · chain A against A, TM-score 1.00
- O75460 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein KINASE/ENDORIBONUCLEASE… · a predicted model of the same protein · chain B 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 O75460
- Elsewhere: RCSB PDB 7BMK · PDBe 7BMK · UniProt O75460
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