Research workbench
EPHB2 / EPHRINA5 complex structure
Analyse EPHB2 / EPHRINA5 complex structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SHW
- Type
- protein
- Length
- 319 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ephrin-A5; Ephrin type-B receptor 2
- UniProt
- O08543, P54763
- Ligands
- NAG, ZN
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ephrin-A5 | protein | 138 | 7% helix, 33% strand | O08543 |
| B | Ephrin type-B receptor 2 | protein | 181 | 3% helix, 47% strand | P54763 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 530 | 0.70 | 0.80 | 56 | empty |
| 2 | 120 | 0.47 | 0.78 | 26 | empty |
| 3 | 72 | 0.40 | 0.79 | 18 | empty |
| 4 | 61 | 0.37 | 0.79 | 19 | empty |
| 5 | 52 | 0.28 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 665 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 1SHW · EphB2 / EphrinA5 Complex Structure · the same entry in another collection · chain A against A, TM-score 1.00
- O08543 · AlphaFold monomer V2.0 prediction for ephrin-A5 (O08543) · a predicted model of the same protein · chain A against A, TM-score 0.96
- 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 0.95
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 O08543
- Every structure of UniProt P54763
- Elsewhere: RCSB PDB 1SHW · PDBe 1SHW · UniProt O08543 · UniProt P54763
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