MolNFT v1 · #86890 · protein
Crystal structure of the human EPHA4 ectodomain in complex with human ephrin A5
4BKA · Ephrin type-a receptor 4: “Crystal structure of the human EPHA4 ectodomain in complex with human ephrin A5”. X-ray diffraction, 6 pockets (best druggability 0.50). MolNFT v1 #86890 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4BKA
- Type
- protein
- Length
- 643 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ephrin type-a receptor 4; Ephrin-A5
- EC
- 2.7.10.1
- UniProt
- P54764, P52803
- Pockets
- 6 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 2% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ephrin type-a receptor 4 (EC 2.7.10.1) | protein | 507 | 0% helix, 36% strand | P54764 |
| C | Ephrin-A5 | protein | 136 | 8% helix, 33% strand | P52803 |
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 126 | 0.50 | 0.81 | 25 | empty |
| 2 | 62 | 0.40 | 0.80 | 17 | empty |
| 3 | 99 | 0.38 | 0.75 | 21 | empty |
| 4 | 111 | 0.37 | 0.74 | 22 | empty |
| 5 | 69 | 0.36 | 0.77 | 12 | empty |
Interfaces
1 interface between chains.
- A–C · 1227 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide (disulfide).
Compared structures
- 4BKA · crystal structure of the human EphA4 ectodomain in complex with human ephrin A5 · the same entry in another collection · chain A against A, TM-score 1.00
- P52803 · AlphaFold monomer V2.0 prediction for ephrin-A5 (P52803) · a predicted model of the same protein · chain C against A, TM-score 0.97
- 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 0.62
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 P52803
- Elsewhere: RCSB PDB 4BKA · PDBe 4BKA · UniProt P54764 · UniProt P52803
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