Research workbench
Nanobody EGB4 bound to the full extracellular EGFR-EGF complex
Analyse Nanobody EGB4 bound to the full extracellular EGFR-EGF complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OM4
- Type
- protein
- Length
- 791 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epidermal growth factor receptor; Epidermal growth factor; Nanobody EGB4
- EC
- 2.7.10.1
- UniProt
- P00533, P01133
- Ligands
- NAG
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 614 | 13% helix, 22% strand | P00533 |
| C | Epidermal growth factor | protein | 47 | 0% helix, 26% strand | P01133 |
| B | Nanobody EGB4 | protein | 130 | 7% helix, 45% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 78 | 0.76 | 0.97 | 21 | empty |
| 2 | 53 | 0.73 | 0.98 | 17 | empty |
| 3 | 650 | 0.70 | 0.78 | 59 | empty |
| 4 | 144 | 0.48 | 0.78 | 30 | empty |
| 5 | 140 | 0.43 | 0.76 | 23 | empty |
Interfaces
2 interfaces between chains.
- A–C · 1547 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 736 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 29 disulfide, 7 glycan (disulfide, N-glycosylation).
Compared structures
- 7OM4 · Nanobody EgB4 bound to the full extracellular EGFR-EGF complex · the same entry in another collection · chain A against A, TM-score 1.00
- P01133 · AlphaFold monomer V2.0 prediction for pro-epidermal growth factor (P01133) · a predicted model of the same protein · chain C against A, TM-score 0.73
- 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 0.52
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 7OM4 · PDBe 7OM4 · UniProt P00533 · UniProt P01133
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