MolNFT v1 · #180946 · protein
Crystal structure of the epidermal growth factor receptor extracellular region with R84K mutation in complex with epiregulin crystallized with spermine
7LFR: “Crystal structure of the epidermal growth factor receptor extracellular region with R84K mutation in complex…”. X-ray diffraction, 3 ligands (NAG, BMA, MAN), 14 pockets (best druggability 0.79). MolNFT v1 #180946 on GenesisL1: 3D…
- PDB
- 7LFR
- Type
- protein
- Length
- 1,093 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epidermal growth factor receptor; Proepiregulin
- EC
- 2.7.10.1
- UniProt
- P00533, O14944
- Ligands
- NAG, BMA, MAN
- Pockets
- 14 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 500 | 15% helix, 23% strand | P00533 |
| B | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 499 | 14% helix, 24% strand | P00533 |
| C, D | Proepiregulin | protein | 47 | 0% helix, 38% strand | O14944 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 564 | 0.79 | 0.85 | 75 | empty |
| 2 | 1018 | 0.77 | 0.79 | 103 | empty |
| 3 | 461 | 0.71 | 0.81 | 56 | empty |
| 4 | 237 | 0.58 | 0.79 | 24 | empty |
| 5 | 101 | 0.46 | 0.79 | 24 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1353 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1349 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1227 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 7LFR · Crystal structure of the epidermal growth factor receptor extracellular region with R84K… · the same entry in another collection · chain D against D, TM-score 1.00
- O14944 · AlphaFold monomer V2.0 prediction for proepiregulin (O14944) · a predicted model of the same protein · chain D against A, TM-score 0.89
- P00533 · AlphaFold monomer V2.0 prediction for epidermal growth factor receptor (P00533) · a predicted model of the same protein · chain B against A, TM-score 0.65
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 P00533
- Every structure of UniProt O14944
- Elsewhere: RCSB PDB 7LFR · PDBe 7LFR · UniProt P00533 · UniProt O14944
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