MolNFT v1 · #74616 · protein
Crystal structure of the human kinase and RNase domains in complex with ADP
3P23 · SERINE/THREONINE-protein KINASE/ENDORIBONUCLEASE IRE1: “Crystal structure of the human kinase and RNase domains in complex with ADP”. X-ray diffraction, 3 ligands (ADP, MG, SO4), 20 pockets (best druggability 0.79). MolNFT v1 #74616…
- 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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