Research workbench
Crystal structure of the EPHA4 lbd in complex with APYD3 peptide inhibitor
Analyse Crystal structure of the EPHA4 lbd in complex with APYD3 peptide inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JR2
- Type
- protein
- Length
- 755 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ephrin type-a receptor 4; APYD3 peptide
- EC
- 2.7.10.1
- UniProt
- P54764
- Ligands
- NH2
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ephrin type-a receptor 4 (EC 2.7.10.1) | protein | 179 | 7% helix, 50% strand | P54764 |
| C | Ephrin type-a receptor 4 (EC 2.7.10.1) | protein | 174 | 7% helix, 52% strand | P54764 |
| D | Ephrin type-a receptor 4 (EC 2.7.10.1) | protein | 175 | 7% helix, 50% strand | P54764 |
| E, F, G, H | APYD3 peptide | protein | 12 | 0% helix, 33% strand | — |
Ligands and binding sites
- NH2 · Amino group · ion · 4 copies · chains E, F, G, H
- GOL · Glycerol · additive · 8 copies · chains A, B, C, D
- HEZ · Hexane-1,6-diol · additive · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 637 | 0.75 | 0.81 | 56 | HEZ |
| 2 | 106 | 0.42 | 0.77 | 26 | empty |
| 3 | 72 | 0.41 | 0.79 | 15 | empty |
| 4 | 65 | 0.40 | 0.80 | 15 | HEZ |
| 5 | 53 | 0.26 | 0.73 | 9 | empty |
Interfaces
11 interfaces between chains.
- C–G · 666 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 662 Ų buried · 9 hydrogen bonds · protein-protein
- B–F · 661 Ų buried · 8 hydrogen bonds · protein-protein
- D–H · 632 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 429 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 8 modified (disulfide, nonstandard).
Compared structures
- 5JR2 · Crystal structure of the EphA4 LBD in complex with APYd3 peptide inhibitor · the same entry in another collection · chain H against H, TM-score 1.00
- P54764 · AlphaFold monomer V2.0 prediction for ephrin type-a receptor 4 (P54764) · a predicted model of the same protein · chain D against A, TM-score 0.90
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
- Elsewhere: RCSB PDB 5JR2 · PDBe 5JR2 · UniProt P54764
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