Research workbench
Crystal structure of the EPHB2 receptor kinase domain in complex with ADP
Analyse Crystal structure of the EPHB2 receptor kinase domain 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
- 2HEN
- Type
- protein
- Length
- 1,036 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ephrin type-B receptor 2
- EC
- 2.7.10.1
- UniProt
- P54763
- Ligands
- ADP, MG
- Pockets
- 9 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Ephrin type-B receptor 2 (EC 2.7.10.1) | protein | 259 | 42% helix, 16% strand | P54763 |
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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 301 | 0.65 | 0.81 | 33 | MG, ADP |
| 2 | 282 | 0.63 | 0.80 | 35 | MG, ADP |
| 3 | 290 | 0.61 | 0.79 | 36 | MG, ADP |
| 4 | 270 | 0.58 | 0.78 | 35 | MG, ADP |
| 5 | 58 | 0.47 | 0.84 | 21 | empty |
Interfaces
2 interfaces between chains.
- A–B · 344 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 302 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2HEN · Crystal Structure of the EphB2 Receptor Kinase domain in complex with ADP · the same entry in another collection · chain D against D, TM-score 1.00
- P54763 · AlphaFold monomer V2.0 prediction for ephrin type-B receptor 2 (P54763) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P54763
- Elsewhere: RCSB PDB 2HEN · PDBe 2HEN · UniProt P54763
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.