Research workbench
Ligand recognition by a-class eph receptors: crystal structures of the EPHA2 ligand-binding domain and the EPHA2/EPHRIN-A1 complex
Analyse Ligand recognition by a-class eph receptors: crystal structures of the EPHA2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HPN
- Type
- protein
- Length
- 1,044 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ephrin type-a receptor 2
- EC
- 2.7.10.1
- UniProt
- P29317
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Ephrin type-a receptor 2 (EC 2.7.10.1) | protein | 174 | 6% helix, 48% strand | P29317 |
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1064 | 0.78 | 0.80 | 87 | empty |
| 2 | 307 | 0.77 | 0.88 | 25 | empty |
| 3 | 294 | 0.76 | 0.87 | 24 | empty |
| 4 | 314 | 0.75 | 0.87 | 26 | empty |
| 5 | 152 | 0.48 | 0.77 | 36 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1356 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1356 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 1343 Ų buried · 20 hydrogen bonds · protein-protein
- B–F · 407 Ų buried · 2 hydrogen bonds · protein-protein
- D–F · 397 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 3HPN · Ligand recognition by A-class EPH receptors: crystal structures of the EPHA2… · the same entry in another collection · chain F against F, TM-score 1.00
- P29317 · AlphaFold monomer V2.0 prediction for ephrin type-a receptor 2 (P29317) · a predicted model of the same protein · chain D against A, TM-score 0.97
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 P29317
- Elsewhere: RCSB PDB 3HPN · PDBe 3HPN · UniProt P29317
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