MolNFT v1 · #10575 · protein
Crystal structure of the complex of human epidermal growth factor and receptor extracellular domains.
1IVO · Epidermal growth factor receptor: “Crystal structure of the complex of human epidermal growth factor and receptor extracellular domains.”. X-ray diffraction, 1 ligand (NAG), 14 pockets (best druggability 0.78). MolNFT v1 #10575 on…
- 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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