MolNFT v1 · #84249 · protein
Crystal structure of EPHB4 in complex with staurosporine
3ZEW · Ephrin type-B receptor 4: “Crystal structure of EPHB4 in complex with staurosporine”. X-ray diffraction, 2 ligands (STU, SO4), 4 pockets (best druggability 0.74). MolNFT v1 #84249 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3ZEW
- Type
- protein
- Length
- 522 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ephrin type-B receptor 4
- EC
- 2.7.10.1
- UniProt
- P54760
- Ligands
- STU, SO4
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ephrin type-B receptor 4 (EC 2.7.10.1) | protein | 270 | 40% helix, 19% strand | P54760 |
| B | Ephrin type-B receptor 4 (EC 2.7.10.1) | protein | 252 | 44% helix, 17% strand | P54760 |
Ligands and binding sites
- STU · Staurosporine · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 309 | 0.74 | 0.86 | 39 | empty |
| 2 | 285 | 0.66 | 0.82 | 33 | STU |
| 3 | 308 | 0.64 | 0.80 | 34 | STU |
| 4 | 404 | 0.60 | 0.76 | 35 | empty |
Interfaces
1 interface between chains.
- A–B · 515 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
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 P54760
- Elsewhere: RCSB PDB 3ZEW · PDBe 3ZEW · UniProt P54760
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