MolNFT v1 · #65465 · protein
Crystal structure of eph receptor and ephrin complex
3GXU · Ephrin type-a receptor 4: “Crystal structure of eph receptor and ephrin complex”. X-ray diffraction, 5 pockets (best druggability 0.50). MolNFT v1 #65465 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3GXU
- Type
- protein
- Length
- 309 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ephrin type-a receptor 4; Ephrin-B2
- EC
- 2.7.10.1
- UniProt
- P54764, P52799
- Pockets
- 5 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ephrin type-a receptor 4 (EC 2.7.10.1) | protein | 171 | 4% helix, 44% strand | P54764 |
| B | Ephrin-B2 | protein | 138 | 7% helix, 28% strand | P52799 |
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 218 | 0.50 | 0.75 | 25 | empty |
| 2 | 129 | 0.49 | 0.79 | 24 | empty |
| 3 | 207 | 0.47 | 0.74 | 26 | empty |
| 4 | 119 | 0.43 | 0.77 | 20 | empty |
| 5 | 50 | 0.33 | 0.78 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1195 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3GXU · Crystal structure of Eph receptor and ephrin 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 0.95
- 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 0.94
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 3GXU · PDBe 3GXU · UniProt P54764 · UniProt P52799
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