Research workbench
Crystal structure of the EPHA4-EPHRINB2 complex
Analyse Crystal structure of the EPHA4-EPHRINB2 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WO2
- Type
- protein
- Length
- 314 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ephrin type-a receptor; Ephrin-B2
- EC
- 2.7.10.1
- UniProt
- P54764, P52799
- Ligands
- NAG
- Pockets
- 4 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ephrin type-a receptor (EC 2.7.10.1) | protein | 178 | 5% helix, 47% strand | P54764 |
| B | Ephrin-B2 | protein | 136 | 8% helix, 32% strand | P52799 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 289 | 0.57 | 0.77 | 28 | empty |
| 2 | 134 | 0.42 | 0.75 | 21 | empty |
| 3 | 101 | 0.36 | 0.75 | 18 | empty |
| 4 | 57 | 0.36 | 0.79 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1283 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 2WO2 · Crystal Structure of the EphA4-ephrinB2 complex · the same entry in another collection · chain A against A, TM-score 1.00
- P52799 · AlphaFold monomer V2.0 prediction for ephrin-B2 (P52799) · a predicted model of the same protein · chain B against A, TM-score 0.97
- P54764 · AlphaFold monomer V2.0 prediction for ephrin type-a receptor 4 (P54764) · a predicted model of the same protein · chain A against A, TM-score 0.92
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 P54764
- Every structure of UniProt P52799
- Elsewhere: RCSB PDB 2WO2 · PDBe 2WO2 · UniProt P54764 · UniProt P52799
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