Research workbench
Structure of oligomeric KINASE/RNASE IRE1 in complex with an oligonucleotide
Analyse Structure of oligomeric KINASE/RNASE IRE1 in complex with an oligonucleotide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SDM
- Type
- protein
- Length
- 2,926 residues
- Chains
- 7
- 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
- P32361
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G | SERINE/THREONINE-protein KINASE/ENDORIBONUCLEASE IRE1 (EC 2.7.11.1, 3.1.26.-) | protein | 418 | 44% helix, 10% strand | P32361 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 755 | 0.77 | 0.82 | 74 | empty |
| 2 | 647 | 0.76 | 0.82 | 77 | empty |
| 3 | 667 | 0.76 | 0.82 | 77 | empty |
| 4 | 634 | 0.75 | 0.82 | 74 | empty |
| 5 | 410 | 0.75 | 0.85 | 42 | empty |
Interfaces
11 interfaces between chains.
- F–G · 2001 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 1985 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1946 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 858 Ų buried · 6 hydrogen bonds · protein-protein
- A–G · 856 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 modified (phosphorylation).
Compared structures
- 3SDM · Structure of oligomeric kinase/RNase Ire1 in complex with an oligonucleotide · the same entry in another collection · chain G against G, TM-score 1.00
- P32361 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein KINASE/ENDORIBONUCLEASE… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P32361
- Elsewhere: RCSB PDB 3SDM · PDBe 3SDM · UniProt P32361
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