MolNFT v1 · #124710 · protein
TGFALPHA/EPIREGULIN complex with neutralizing antibody LY3016859
5KN5 · Epiregulin antibody LY3016859 Fab heavy chain: “TGFALPHA/EPIREGULIN complex with neutralizing antibody LY3016859”. X-ray diffraction, 2 ligands (ZN, SO4), 8 pockets (best druggability 0.64). MolNFT v1 #124710 on GenesisL1: 3D…
- PDB
- 5KN5
- Type
- protein
- Length
- 940 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epiregulin antibody LY3016859 Fab heavy chain; Epiregulin antibody LY3016859 Fab light…
- UniProt
- P01135
- Ligands
- ZN, SO4
- Pockets
- 8 · best druggability 0.64
Structure
x-ray diffraction · 5 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epiregulin antibody LY3016859 Fab heavy chain | protein | 214 | 7% helix, 52% strand | — |
| B, E | Epiregulin antibody LY3016859 Fab light chain | protein | 216 | 6% helix, 50% strand | — |
| C | Protransforming growth factor alpha | protein | 40 | 0% helix, 43% strand | P01135 |
| D | Epiregulin antibody LY3016859 Fab heavy chain | protein | 215 | 8% helix, 52% strand | — |
| F | Protransforming growth factor alpha | protein | 39 | 0% helix, 44% strand | P01135 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 337 | 0.64 | 0.80 | 56 | empty |
| 2 | 396 | 0.56 | 0.74 | 51 | empty |
| 3 | 311 | 0.55 | 0.76 | 44 | empty |
| 4 | 79 | 0.32 | 0.74 | 15 | empty |
| 5 | 60 | 0.29 | 0.74 | 18 | empty |
Interfaces
10 interfaces between chains.
- D–E · 1876 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1838 Ų buried · 14 hydrogen bonds · protein-protein
- D–F · 554 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 516 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 408 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 5KN5 · TGFalpha/Epiregulin complex with neutralizing antibody LY3016859 · the same entry in another collection · chain F against F, TM-score 1.00
- P01135 · AlphaFold monomer V2.0 prediction for protransforming growth factor alpha (P01135) · a predicted model of the same protein · chain C against A, TM-score 0.78
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 P01135
- Elsewhere: RCSB PDB 5KN5 · PDBe 5KN5 · UniProt P01135
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