Research workbench
Crystal structure of the complex of human epidermal growth factor and receptor extracellular domains.
Analyse Crystal structure of the complex of human epidermal growth factor and receptor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1IVO
- Type
- protein
- Length
- 1,115 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epidermal growth factor receptor; Epidermal growth factor
- EC
- 2.7.1.112
- UniProt
- P00533, P01133
- Ligands
- NAG
- Pockets
- 14 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epidermal growth factor receptor (EC 2.7.1.112) | protein | 511 | 12% helix, 18% strand | P00533 |
| B | Epidermal growth factor receptor (EC 2.7.1.112) | protein | 510 | 11% helix, 22% strand | P00533 |
| C, D | Epidermal growth factor | protein | 47 | 6% helix, 32% strand | P01133 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 741 | 0.78 | 0.82 | 73 | empty |
| 2 | 1117 | 0.76 | 0.79 | 87 | empty |
| 3 | 1052 | 0.76 | 0.79 | 92 | empty |
| 4 | 558 | 0.66 | 0.76 | 43 | empty |
| 5 | 173 | 0.58 | 0.82 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1607 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 1571 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1415 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 42 disulfide, 9 glycan (disulfide, N-glycosylation).
Compared structures
- 1IVO · Crystal Structure of the Complex of Human Epidermal Growth Factor and Receptor… · the same entry in another collection · chain D against D, TM-score 1.00
- P01133 · AlphaFold monomer V2.0 prediction for pro-epidermal growth factor (P01133) · a predicted model of the same protein · chain D against A, TM-score 0.80
- 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 0.63
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 P01133
- Elsewhere: RCSB PDB 1IVO · PDBe 1IVO · UniProt P00533 · UniProt P01133
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