MolNFT v1 · #180947 · protein
Crystal structure of the epidermal growth factor receptor extracellular region with A265V mutation in complex with epiregulin
7LFS · Isoform 4 of epidermal growth factor receptor: “Crystal structure of the epidermal growth factor receptor extracellular region with A265V mutation in complex…”. X-ray diffraction, 3 ligands (NAG, MAN, BMA), 20 pockets (best…
- PDB
- 7LFS
- Type
- protein
- Length
- 2,184 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoform 4 of epidermal growth factor receptor; Proepiregulin
- EC
- 2.7.10.1
- UniProt
- P00533, O14944
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 7 distinct chains · 11% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Isoform 4 of epidermal growth factor receptor (EC 2.7.10.1) | protein | 500 | 10% helix, 22% strand | P00533 |
| B | Isoform 4 of epidermal growth factor receptor (EC 2.7.10.1) | protein | 503 | 13% helix, 23% strand | P00533 |
| D | Isoform 4 of epidermal growth factor receptor (EC 2.7.10.1) | protein | 498 | 12% helix, 21% strand | P00533 |
| E | Proepiregulin | protein | 48 | 0% helix, 40% strand | O14944 |
| F | Proepiregulin | protein | 45 | 0% helix, 42% strand | O14944 |
| G | Proepiregulin | protein | 46 | 0% helix, 39% strand | O14944 |
| H | Proepiregulin | protein | 44 | 0% helix, 27% strand | O14944 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, B, C, D
- MAN · alpha-D-mannopyranose · sugar · 5 copies · chains A, B, C
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 111 | 0.77 | 0.96 | 25 | empty |
| 2 | 1184 | 0.75 | 0.78 | 94 | empty |
| 3 | 451 | 0.74 | 0.83 | 50 | empty |
| 4 | 476 | 0.71 | 0.81 | 52 | empty |
| 5 | 532 | 0.71 | 0.80 | 79 | empty |
Interfaces
9 interfaces between chains.
- B–F · 1365 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1326 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 1320 Ų buried · 14 hydrogen bonds · protein-protein
- C–G · 1231 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 1049 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 79 disulfide, 11 glycan (disulfide, N-glycosylation).
Compared structures
- 7LFS · Crystal structure of the epidermal growth factor receptor extracellular region with A265V… · the same entry in another collection · chain H against H, TM-score 1.00
- O14944 · AlphaFold monomer V2.0 prediction for proepiregulin (O14944) · a predicted model of the same protein · chain H 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 P00533
- Every structure of UniProt O14944
- Elsewhere: RCSB PDB 7LFS · PDBe 7LFS · UniProt P00533 · UniProt O14944
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