Research workbench
The extracellular and transmembrane domain interfaces in epidermal growth factor receptor signaling
Analyse The extracellular and transmembrane domain interfaces in epidermal growth… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NJP
- Type
- protein
- Length
- 1,322 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epidermal growth factor receptor; Epidermal growth factor
- EC
- 2.7.10.1
- UniProt
- P00533, Q6QBS2
- Ligands
- NAG
- Pockets
- 15 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 614 | 13% helix, 26% strand | P00533 |
| C, D | Epidermal growth factor | protein | 47 | 0% helix, 32% strand | Q6QBS2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B
- 2PE · Nonaethylene glycol · additive · 5 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 961 | 0.78 | 0.80 | 71 | empty |
| 2 | 1171 | 0.77 | 0.79 | 88 | empty |
| 3 | 1040 | 0.77 | 0.79 | 81 | empty |
| 4 | 405 | 0.63 | 0.77 | 42 | empty |
| 5 | 156 | 0.53 | 0.80 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1758 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 1612 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1575 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 56 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 3NJP · The Extracellular and Transmembrane Domain Interfaces in Epidermal Growth Factor Receptor… · the same entry in another collection · chain A against A, TM-score 1.00
- 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 0.53
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 Q6QBS2
- Elsewhere: RCSB PDB 3NJP · PDBe 3NJP · UniProt P00533 · UniProt Q6QBS2
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