MolNFT v1 · #31935 · protein
Crystal structure and thermodynamic characterization of the EPHB4 receptor in complex with an ephrin-B2 antagonist peptide reveals the determinants for receptor specificity.
2BBA · Ephrin type-B receptor 4: “Crystal structure and thermodynamic characterization of the EPHB4 receptor in complex with an ephrin-B2…”. X-ray diffraction, 1 ligand (SO4), 1 pocket (best druggability 0.37). MolNFT v1 #31935 on…
- PDB
- 2BBA
- Type
- protein
- Length
- 199 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ephrin type-B receptor 4; Agonist peptide
- EC
- 2.7.1.112
- UniProt
- P54760
- Ligands
- SO4
- Pockets
- 1 · best druggability 0.37
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ephrin type-B receptor 4 (EC 2.7.1.112) | protein | 185 | 3% helix, 48% strand | P54760 |
| P | Agonist peptide | protein | 14 | 21% helix, 0% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 80 | 0.37 | 0.77 | 13 | empty |
Interfaces
1 interface between chains.
- A–P · 712 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2BBA · Crystal Structure and Thermodynamic Characterization of the EphB4 Receptor in Complex… · the same entry in another collection · chain A against A, TM-score 1.00
- P54760 · AlphaFold monomer V2.0 prediction for ephrin type-B receptor 4 (P54760) · a predicted model of the same protein · chain A 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 P54760
- Elsewhere: RCSB PDB 2BBA · PDBe 2BBA · UniProt P54760
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