Research workbench
Crystal structure of EPHA2 ectodomain in complex with ephrin-A5
Analyse Crystal structure of EPHA2 ectodomain in complex with ephrin-A5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MX0
- Type
- protein
- Length
- 1,088 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ephrin type-a receptor 2; Ephrin-A5
- EC
- 2.7.10.1
- UniProt
- P29317, P52803
- Ligands
- NAG
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 2% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Ephrin type-a receptor 2 (EC 2.7.10.1) | protein | 406 | 1% helix, 34% strand | P29317 |
| B, D | Ephrin-A5 | protein | 138 | 4% helix, 27% strand | P52803 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains B, D, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 894 | 0.79 | 0.82 | 92 | empty |
| 2 | 364 | 0.58 | 0.76 | 34 | empty |
| 3 | 258 | 0.55 | 0.77 | 40 | empty |
| 4 | 128 | 0.46 | 0.78 | 27 | empty |
| 5 | 122 | 0.41 | 0.76 | 20 | empty |
Interfaces
5 interfaces between chains.
- C–D · 957 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 891 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 554 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 101 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 81 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 3MX0 · Crystal Structure of EphA2 ectodomain in complex with ephrin-A5 · the same entry in another collection · chain D against D, TM-score 1.00
- P52803 · AlphaFold monomer V2.0 prediction for ephrin-A5 (P52803) · a predicted model of the same protein · chain D against A, TM-score 0.96
- 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 0.95
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 P52803
- Elsewhere: RCSB PDB 3MX0 · PDBe 3MX0 · UniProt P29317 · UniProt P52803
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