MolNFT v1 · #53222 · protein
Crystal structure of the EPHA4-EPHRINA2 complex
2WO3 · Ephrin type-a receptor: “Crystal structure of the EPHA4-EPHRINA2 complex”. X-ray diffraction, 1 ligand (NAG), 4 pockets (best druggability 0.69). MolNFT v1 #53222 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2WO3
- Type
- protein
- Length
- 318 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ephrin type-a receptor; Ephrin-A2
- EC
- 2.7.10.1
- UniProt
- P54764, O43921
- Ligands
- NAG
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ephrin type-a receptor (EC 2.7.10.1) | protein | 176 | 7% helix, 48% strand | P54764 |
| B | Ephrin-A2 | protein | 142 | 6% helix, 32% strand | O43921 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · 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 | 338 | 0.69 | 0.82 | 56 | empty |
| 2 | 110 | 0.44 | 0.78 | 16 | empty |
| 3 | 93 | 0.33 | 0.73 | 17 | empty |
| 4 | 60 | 0.31 | 0.76 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1041 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 2WO3 · Crystal Structure of the EphA4-ephrinA2 complex · the same entry in another collection · chain A against A, TM-score 1.00
- O43921 · AlphaFold monomer V2.0 prediction for ephrin-A2 (O43921) · a predicted model of the same protein · chain B against A, TM-score 0.99
- 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 0.99
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 O43921
- Elsewhere: RCSB PDB 2WO3 · PDBe 2WO3 · UniProt P54764 · UniProt O43921
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