MolNFT v1 · #38952 · protein
Crystal structure of the EPHB2 receptor kinase domain in complex with ADP
2HEN · Ephrin type-B receptor 2: “Crystal structure of the EPHB2 receptor kinase domain in complex with ADP”. X-ray diffraction, 2 ligands (ADP, MG), 9 pockets (best druggability 0.65). MolNFT v1 #38952 on GenesisL1: 3D structure, binding…
- 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
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