Research workbench
Crystal structure of human phosphorylated IRE1ALPHA in complex with ADP-mg
Analyse Crystal structure of human phosphorylated IRE1ALPHA in complex with ADP-mg in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YZD
- Type
- protein
- Length
- 1,147 residues
- Chains
- 3
- 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
- ADP, MG
- Pockets
- 19 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 15% 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 | 383 | 43% helix, 15% strand | O75460 |
| B | SERINE/THREONINE-protein KINASE/ENDORIBONUCLEASE IRE1 (EC 2.7.11.1, 3.1.26.-) | protein | 385 | 42% helix, 14% strand | O75460 |
| C | SERINE/THREONINE-protein KINASE/ENDORIBONUCLEASE IRE1 (EC 2.7.11.1, 3.1.26.-) | protein | 379 | 44% helix, 15% strand | O75460 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 370 | 0.73 | 0.84 | 39 | MG, ADP |
| 2 | 287 | 0.66 | 0.82 | 33 | MG, ADP |
| 3 | 249 | 0.65 | 0.82 | 35 | ADP |
| 4 | 174 | 0.64 | 0.84 | 29 | empty |
| 5 | 161 | 0.58 | 0.82 | 25 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1202 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 267 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4YZD · Crystal Structure of human phosphorylated IRE1alpha in complex with ADP-Mg · 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 A 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 O75460
- Elsewhere: RCSB PDB 4YZD · PDBe 4YZD · UniProt O75460
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