Research workbench
Crystal structure of the drosophila epidermal growth factor receptor ectodomain in complex with spitz
Analyse Crystal structure of the drosophila epidermal growth factor receptor ectodomain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LTF
- Type
- protein
- Length
- 1,167 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epidermal growth factor receptor; Protein spitz
- EC
- 2.7.10.-
- UniProt
- P04412, Q01083
- Ligands
- NAG, MAN
- Pockets
- 14 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epidermal growth factor receptor (EC 2.7.10.-) | protein | 522 | 12% helix, 28% strand | P04412 |
| C | Epidermal growth factor receptor (EC 2.7.10.-) | protein | 531 | 9% helix, 29% strand | P04412 |
| D, B | Protein spitz | protein | 57 | 11% helix, 35% strand | Q01083 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, C
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains A, C
- MLI · Malonate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1135 | 0.78 | 0.80 | 100 | empty |
| 2 | 1144 | 0.76 | 0.79 | 95 | empty |
| 3 | 1011 | 0.73 | 0.76 | 97 | empty |
| 4 | 239 | 0.65 | 0.83 | 37 | empty |
| 5 | 153 | 0.50 | 0.78 | 24 | empty |
Interfaces
3 interfaces between chains.
- C–D · 2104 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1927 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 1790 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 47 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 3LTF · Crystal Structure of the Drosophila Epidermal Growth Factor Receptor ectodomain in… · the same entry in another collection · chain A against A, TM-score 1.00
- Q01083 · AlphaFold monomer V2.0 prediction for protein spitz (Q01083) · a predicted model of the same protein · chain D against A, TM-score 0.90
- P04412 · AlphaFold monomer V2.0 prediction for epidermal growth factor receptor (P04412) · a predicted model of the same protein · chain A 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 P04412
- Every structure of UniProt Q01083
- Elsewhere: RCSB PDB 3LTF · PDBe 3LTF · UniProt P04412 · UniProt Q01083
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