Research workbench
Structure of the EPHA4 lbd in complex with peptide
Analyse Structure of the EPHA4 lbd in complex with peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4W4Z
- Type
- protein
- Length
- 747 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ephrin type-a receptor 4; Apy-BALA8.AM peptide
- EC
- 2.7.10.1
- UniProt
- P54764
- Ligands
- NH2
- Pockets
- 11 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 3% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ephrin type-a receptor 4 (EC 2.7.10.1) | protein | 176 | 3% helix, 51% strand | P54764 |
| C | Ephrin type-a receptor 4 (EC 2.7.10.1) | protein | 174 | 3% helix, 52% strand | P54764 |
| D | Ephrin type-a receptor 4 (EC 2.7.10.1) | protein | 173 | 3% helix, 53% strand | P54764 |
| E, F, G, H | Apy-BALA8.AM 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 · 14 copies · chains A, D, B, F, C, H
- HEZ · Hexane-1,6-diol · additive · 7 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 324 | 0.70 | 0.84 | 32 | HEZ, GOL |
| 2 | 551 | 0.70 | 0.79 | 58 | HEZ, GOL |
| 3 | 383 | 0.60 | 0.76 | 48 | empty |
| 4 | 192 | 0.52 | 0.78 | 27 | GOL |
| 5 | 148 | 0.50 | 0.79 | 22 | GOL, HEZ |
Interfaces
11 interfaces between chains.
- B–F · 642 Ų buried · 5 hydrogen bonds · protein-protein
- D–H · 642 Ų buried · 8 hydrogen bonds · protein-protein
- C–G · 633 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 625 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 582 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 4 modified (disulfide, nonstandard).
Compared structures
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 4W4Z · PDBe 4W4Z · UniProt P54764
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