Research workbench
Crystal structure of del-1 EGF domains
Analyse Crystal structure of del-1 EGF domains in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4D90
- Type
- protein
- Length
- 253 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- EGF-like repeat and discoidin I-like domain-containing protein 3
- UniProt
- O43854
- Ligands
- NGA, NAG, FUC, CA
- Pockets
- 3 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | EGF-like repeat and discoidin I-like domain-containing protein 3 | protein | 127 | 2% helix, 27% strand | O43854 |
| B | EGF-like repeat and discoidin I-like domain-containing protein 3 | protein | 126 | 5% helix, 30% strand | O43854 |
Ligands and binding sites
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 165 | 0.56 | 0.81 | 28 | empty |
| 2 | 152 | 0.46 | 0.76 | 26 | empty |
| 3 | 109 | 0.44 | 0.78 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1582 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 6 glycan (disulfide, O-glycosylation, N-glycosylation).
Compared structures
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 O43854
- Elsewhere: RCSB PDB 4D90 · PDBe 4D90 · UniProt O43854
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