MolNFT v1 · #117442 · protein
Crystal structure of human epiregulin in complex with the Fab fragment of murine monoclonal antibody 9E5
5E8D · Proepiregulin: “Crystal structure of human epiregulin in complex with the Fab fragment of murine monoclonal antibody 9E5”. X-ray diffraction, 1 ligand (CL), 3 pockets (best druggability 0.52). MolNFT v1 #117442 on GenesisL1: 3D…
- 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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