MolNFT v1 · #59163 · protein
Crystal structure of catalytic domain of the proto-oncogene tyrosine- protein kinase mer in complex with inhibitor C52
3BPR · Proto-oncogene tyrosine-protein kinase mer: “Crystal structure of catalytic domain of the proto-oncogene tyrosine- protein kinase mer in complex with…”. X-ray diffraction, 3 ligands (OLP, NA, CL), 7 pockets (best druggability 0.75).…
- PDB
- 3BPR
- Type
- protein
- Length
- 1,035 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proto-oncogene tyrosine-protein kinase mer
- EC
- 2.7.10.1
- UniProt
- Q12866
- Ligands
- OLP, NA, CL
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proto-oncogene tyrosine-protein kinase mer (EC 2.7.10.1) | protein | 261 | 41% helix, 17% strand | Q12866 |
| B | Proto-oncogene tyrosine-protein kinase mer (EC 2.7.10.1) | protein | 256 | 41% helix, 17% strand | Q12866 |
| C | Proto-oncogene tyrosine-protein kinase mer (EC 2.7.10.1) | protein | 259 | 41% helix, 17% strand | Q12866 |
| D | Proto-oncogene tyrosine-protein kinase mer (EC 2.7.10.1) | protein | 259 | 41% helix, 17% strand | Q12866 |
Ligands and binding sites
- OLP · 2-(2-hydroxyethylamino)-6-(3-chloroanilino)-9-isopropylpurine · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · chains A, B
- CL · Chloride ion · ion · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1106 | 0.75 | 0.77 | 106 | OLP |
| 2 | 338 | 0.62 | 0.78 | 35 | OLP |
| 3 | 293 | 0.61 | 0.79 | 33 | empty |
| 4 | 477 | 0.60 | 0.75 | 55 | empty |
| 5 | 314 | 0.60 | 0.78 | 36 | OLP |
Interfaces
3 interfaces between chains.
- A–B · 1149 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 452 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 93 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3BPR · Crystal structure of catalytic domain of the proto-oncogene tyrosine-protein kinase MER… · the same entry in another collection · chain D against D, TM-score 1.00
- Q12866 · AlphaFold monomer V2.0 prediction for tyrosine-protein kinase mer (Q12866) · a predicted model of the same protein · chain B 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 Q12866
- Elsewhere: RCSB PDB 3BPR · PDBe 3BPR · UniProt Q12866
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