Research workbench
Structure of RNase-inactive point mutant of oligomeric KINASE/RNASE IRE1
Analyse Structure of RNase-inactive point mutant of oligomeric KINASE/RNASE IRE1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SDJ
- Type
- protein
- Length
- 5,862 residues
- Chains
- 14
- 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
- Ligands
- APJ
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E, F, G, H, L, M, N | SERINE/THREONINE-protein KINASE/ENDORIBONUCLEASE IRE1 (EC 2.7.11.1, 3.1.26.-) | protein | 418 | 42% helix, 11% strand | P32361 |
| D, K | SERINE/THREONINE-protein KINASE/ENDORIBONUCLEASE IRE1 (EC 2.7.11.1, 3.1.26.-) | protein | 425 | 40% helix, 11% strand | P32361 |
| I, J | SERINE/THREONINE-protein KINASE/ENDORIBONUCLEASE IRE1 (EC 2.7.11.1, 3.1.26.-) | protein | 416 | 42% helix, 12% strand | P32361 |
Ligands and binding sites
- APJ · N~2~-1H-benzimidazol-5-yl-N~4~-(3-cyclopropyl-1H-pyrazol-5-yl)pyrimidine-2,4-diamine · ligand · 14 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 864 | 0.81 | 0.83 | 99 | APJ |
| 2 | 1078 | 0.78 | 0.80 | 106 | APJ |
| 3 | 1186 | 0.78 | 0.80 | 111 | APJ |
| 4 | 836 | 0.78 | 0.81 | 87 | empty |
| 5 | 669 | 0.76 | 0.82 | 78 | empty |
Interfaces
25 interfaces between chains.
- G–H · 2076 Ų buried · 32 hydrogen bonds · protein-protein
- M–N · 2041 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 2039 Ų buried · 30 hydrogen bonds · protein-protein
- E–F · 2027 Ų buried · 28 hydrogen bonds · protein-protein
- K–L · 2002 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 42 modified (phosphorylation).
Compared structures
- 3SDJ · Structure of RNase-inactive point mutant of oligomeric kinase/RNase Ire1 · the same entry in another collection · chain N against N, TM-score 1.00
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 3SDJ · PDBe 3SDJ · UniProt P32361
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.