Research workbench
Crystal structure of the human kinase and RNase domains in complex with ADP
Analyse Crystal structure of the human kinase and RNase domains in complex with ADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3P23
- Type
- protein
- Length
- 1,549 residues
- Chains
- 4
- 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, SO4
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 41% 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 | 386 | 40% helix, 16% strand | O75460 |
| B | SERINE/THREONINE-protein KINASE/ENDORIBONUCLEASE IRE1 (EC 2.7.11.1, 3.1.26.-) | protein | 386 | 43% helix, 13% strand | O75460 |
| C | SERINE/THREONINE-protein KINASE/ENDORIBONUCLEASE IRE1 (EC 2.7.11.1, 3.1.26.-) | protein | 390 | 42% helix, 13% strand | O75460 |
| D | SERINE/THREONINE-protein KINASE/ENDORIBONUCLEASE IRE1 (EC 2.7.11.1, 3.1.26.-) | protein | 387 | 41% helix, 12% strand | O75460 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 221 | 0.79 | 0.93 | 29 | empty |
| 2 | 595 | 0.71 | 0.79 | 44 | SO4 |
| 3 | 335 | 0.69 | 0.82 | 37 | MG, ADP |
| 4 | 509 | 0.68 | 0.79 | 58 | MG, ADP |
| 5 | 340 | 0.65 | 0.80 | 36 | MG, ADP |
Interfaces
3 interfaces between chains.
- C–D · 922 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 878 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 873 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3P23 · Crystal structure of the Human kinase and RNase domains in complex with ADP · the same entry in another collection · chain D against D, TM-score 1.00
- O75460 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein KINASE/ENDORIBONUCLEASE… · a predicted model of the same protein · chain D against A, TM-score 0.94
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 3P23 · PDBe 3P23 · UniProt O75460
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