Research workbench
Crystal structure of human epiregulin in complex with the Fab fragment of murine monoclonal antibody 9E5
Analyse Crystal structure of human epiregulin in complex with the Fab fragment of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5E8D
- Type
- protein
- Length
- 469 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proepiregulin; Anti-human epiregulin antibody 9E5 Fab heavy chain; Anti-human epiregulin…
- UniProt
- O14944
- Ligands
- CL
- Pockets
- 3 · best druggability 0.52
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proepiregulin | protein | 43 | 7% helix, 42% strand | O14944 |
| H | Anti-human epiregulin antibody 9E5 Fab heavy chain | protein | 216 | 8% helix, 53% strand | — |
| L | Anti-human epiregulin antibody 9E5 Fab light chain | protein | 210 | 4% helix, 46% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 348 | 0.52 | 0.73 | 47 | empty |
| 2 | 176 | 0.44 | 0.74 | 26 | empty |
| 3 | 74 | 0.34 | 0.76 | 17 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1778 Ų buried · 16 hydrogen bonds · protein-protein
- A–H · 535 Ų buried · 15 hydrogen bonds · protein-protein
- A–L · 489 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 5E8D · Crystal structure of human epiregulin in complex with the Fab fragment of murine… · the same entry in another collection · chain A against A, TM-score 1.00
- O14944 · AlphaFold monomer V2.0 prediction for proepiregulin (O14944) · a predicted model of the same protein · chain A 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 O14944
- Elsewhere: RCSB PDB 5E8D · PDBe 5E8D · UniProt O14944
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