MolNFT v1 · #98153 · protein
Structure of the human EPHA3 receptor ligand binding domain complexed with ephrin-A5
4L0P · Ephrin type-a receptor 3: “Structure of the human EPHA3 receptor ligand binding domain complexed with ephrin-A5”. X-ray diffraction, 3 ligands (NAG, CA, SO4), 6 pockets (best druggability 0.54). MolNFT v1 #98153 on GenesisL1: 3D…
- PDB
- 4L0P
- Type
- protein
- Length
- 314 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ephrin type-a receptor 3; Ephrin-A5
- UniProt
- P29320, P52803
- Ligands
- NAG, CA, SO4
- Pockets
- 6 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ephrin type-a receptor 3 | protein | 175 | 7% helix, 47% strand | P29320 |
| B | Ephrin-A5 | protein | 139 | 12% helix, 35% strand | P52803 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B
- CA · Calcium ion · metal · chains B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 153 | 0.54 | 0.80 | 21 | empty |
| 2 | 84 | 0.52 | 0.84 | 26 | empty |
| 3 | 104 | 0.45 | 0.79 | 22 | empty |
| 4 | 98 | 0.42 | 0.77 | 27 | empty |
| 5 | 125 | 0.37 | 0.73 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1377 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 4L0P · Structure of the human EphA3 receptor ligand binding domain complexed with 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 B against A, TM-score 0.99
- P29320 · AlphaFold monomer V2.0 prediction for ephrin type-a receptor 3 (P29320) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 P29320
- Every structure of UniProt P52803
- Elsewhere: RCSB PDB 4L0P · PDBe 4L0P · UniProt P29320 · UniProt P52803
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