Research workbench
Crystal structure of the human ephrin A2- ephrin A1 complex
Analyse Crystal structure of the human ephrin A2- ephrin A1 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CZU
- Type
- protein
- Length
- 305 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ephrin type-a receptor 2; Ephrin-A1
- EC
- 2.7.10.1
- UniProt
- P29317, P20827
- Ligands
- NAG, MAN
- Pockets
- 4 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ephrin type-a receptor 2 (EC 2.7.10.1) | protein | 175 | 8% helix, 49% strand | P29317 |
| B | Ephrin-A1 | protein | 130 | 12% helix, 34% strand | P20827 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B
- MAN · alpha-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 170 | 0.49 | 0.77 | 25 | empty |
| 2 | 175 | 0.44 | 0.75 | 28 | empty |
| 3 | 67 | 0.38 | 0.79 | 17 | empty |
| 4 | 71 | 0.36 | 0.77 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1200 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 3CZU · Crystal structure of the human ephrin A2- ephrin A1 complex · the same entry in another collection · chain A against A, 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 A against A, TM-score 0.99
- P20827 · AlphaFold monomer V2.0 prediction for ephrin-A1 (P20827) · a predicted model of the same protein · chain B 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
- Every structure of UniProt P20827
- Elsewhere: RCSB PDB 3CZU · PDBe 3CZU · UniProt P29317 · UniProt P20827
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