Research workbench
Crystal structure of the inactive EGFR kinase domain in complex with AMP-pnp
Analyse Crystal structure of the inactive EGFR kinase domain in complex with AMP-pnp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GS7
- Type
- protein
- Length
- 569 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epidermal growth factor receptor
- EC
- 2.7.10.1
- UniProt
- P00533
- Ligands
- ANP, MG, IOD
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 281 | 37% helix, 17% strand | P00533 |
| B | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 288 | 36% helix, 17% strand | P00533 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- IOD · Iodide ion · ion · 11 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 518 | 0.75 | 0.82 | 61 | MG, IOD, ANP |
| 2 | 433 | 0.72 | 0.82 | 49 | MG, ANP |
| 3 | 120 | 0.66 | 0.88 | 27 | IOD |
| 4 | 106 | 0.43 | 0.78 | 23 | empty |
| 5 | 54 | 0.27 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1134 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 2GS7 · Crystal Structure of the inactive EGFR kinase domain in complex with AMP-PNP · 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 A against A, TM-score 0.92
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 2GS7 · PDBe 2GS7 · UniProt P00533
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