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Crystal structure of ephrin A2 (EPHA2) receptor protein kinase with alisertib (MLN8237)
Analyse Crystal structure of ephrin A2 (EPHA2) receptor protein kinase with alisertib… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IA0
- Type
- protein
- Length
- 798 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ephrin type-a receptor 2
- EC
- 2.7.10.1
- UniProt
- P29317
- Ligands
- A5B
- Pockets
- 10 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ephrin type-a receptor 2 (EC 2.7.10.1) | protein | 263 | 44% helix, 16% strand | P29317 |
| B | Ephrin type-a receptor 2 (EC 2.7.10.1) | protein | 266 | 42% helix, 17% strand | P29317 |
| C | Ephrin type-a receptor 2 (EC 2.7.10.1) | protein | 269 | 43% helix, 16% strand | P29317 |
Ligands and binding sites
- A5B · alisertib · ligand · 3 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 20 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 386 | 0.61 | 0.77 | 40 | A5B |
| 2 | 342 | 0.60 | 0.77 | 40 | A5B, EDO |
| 3 | 316 | 0.60 | 0.78 | 32 | A5B |
| 4 | 249 | 0.57 | 0.78 | 37 | EDO |
| 5 | 229 | 0.53 | 0.77 | 31 | empty |
Interfaces
3 interfaces between chains.
- A–B · 543 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 425 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 161 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5IA0 · Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase with alisertib (MLN8237) · the same entry in another collection · chain A against A, TM-score 1.00
- P29317 · AlphaFold monomer V2.0 prediction for ephrin type-a receptor 2 (P29317) · a predicted model of the same protein · chain B 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 P29317
- Elsewhere: RCSB PDB 5IA0 · PDBe 5IA0 · UniProt P29317
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