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
- 3GT8
- Type
- protein
- Length
- 1,194 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epidermal growth factor receptor; Unknown peptide
- EC
- 2.7.10.1
- UniProt
- P00533
- Ligands
- ANP, MG
- Pockets
- 19 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 39% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 292 | 39% helix, 16% strand | P00533 |
| A | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 300 | 37% helix, 15% strand | P00533 |
| C | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 296 | 40% helix, 17% strand | P00533 |
| D | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 295 | 39% helix, 17% strand | P00533 |
| X | Unknown peptide | protein | 11 | 0% helix, 0% strand | — |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 4 copies · chains B, A, C, D
- MG · Magnesium ion · metal · 4 copies · chains B, A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 955 | 0.82 | 0.83 | 85 | ANP, MG |
| 2 | 409 | 0.76 | 0.85 | 33 | empty |
| 3 | 545 | 0.75 | 0.83 | 65 | ANP, MG |
| 4 | 373 | 0.70 | 0.82 | 52 | ANP, MG |
| 5 | 71 | 0.67 | 0.94 | 21 | empty |
Interfaces
5 interfaces between chains.
- A–D · 1678 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1676 Ų buried · 24 hydrogen bonds · protein-protein
- B–X · 368 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 356 Ų buried · 4 hydrogen bonds · protein-protein
- C–X · 80 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3GT8 · Crystal structure of the inactive EGFR kinase domain in complex with AMP-PNP · the same entry in another collection · chain X against X, 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 0.89
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 3GT8 · PDBe 3GT8 · UniProt P00533
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