Research workbench
Crystal structure of EGFR 696-1022 T790M/V948R in complex with SKLB(3)
Analyse Crystal structure of EGFR 696-1022 T790M/V948R in complex with SKLB(3) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5X2A
- Type
- protein
- Length
- 1,219 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.85
- Source
- Homo sapiens
- Molecule
- Epidermal growth factor receptor
- EC
- 2.7.10.1
- UniProt
- P00533
- Ligands
- 7XO, ANP, MG, CL
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · resolution 1.85 · 4 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 297 | 44% helix, 18% strand | P00533 |
| B | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 322 | 42% helix, 15% strand | P00533 |
| C | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 303 | 43% helix, 16% strand | P00533 |
| D | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 297 | 42% helix, 16% strand | P00533 |
Ligands and binding sites
- 7XO · N2-[4-(4-methylpiperazin-1-yl)phenyl]-N8-phenyl-9-propan-2-yl-purine-2,8-diamine · ligand · 3 copies · chains A, B, C
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 3 copies · chains A, B, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, D
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 12 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 822 | 0.81 | 0.84 | 86 | 7XO, ANP, MG |
| 2 | 354 | 0.80 | 0.89 | 26 | empty |
| 3 | 845 | 0.80 | 0.82 | 80 | MG, ANP |
| 4 | 690 | 0.78 | 0.83 | 88 | 7XO |
| 5 | 65 | 0.72 | 0.97 | 15 | empty |
Interfaces
4 interfaces between chains.
- B–C · 2141 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 1589 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 443 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 288 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5X2A · Crystal structure of EGFR 696-1022 T790M/V948R in complex with SKLB(3) · the same entry in another collection · chain D against D, TM-score 1.00
- P00533 · AlphaFold monomer V2.0 prediction for epidermal growth factor receptor (P00533) · a predicted model of the same protein · chain A against A, TM-score 0.89
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
- Elsewhere: RCSB PDB 5X2A · PDBe 5X2A · UniProt P00533
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