Research workbench
Crystal structure of discoidin I from dictyostelium discoideum in complex with the disaccharide galnac beta 1-3 galactose, at 1.6 a resolution.
Analyse Crystal structure of discoidin I from dictyostelium discoideum in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WN3
- Type
- protein
- Length
- 759 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Discoidin-1 subunit a
- UniProt
- P02886
- Ligands
- 1PG, GAL, NGA, CA, SO4
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Discoidin-1 subunit a | protein | 254 | 6% helix, 52% strand | P02886 |
| B | Discoidin-1 subunit a | protein | 253 | 5% helix, 52% strand | P02886 |
| C | Discoidin-1 subunit a | protein | 252 | 5% helix, 52% strand | P02886 |
Ligands and binding sites
- 1PG · 2-(2-{2-[2-(2-methoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethanol · ligand · chains A
- GAL · beta-D-galactopyranose · sugar · 3 copies · chains B, C, A
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · 3 copies · chains A, B, C
- CA · Calcium ion · metal · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 260 | 0.75 | 0.88 | 52 | empty |
| 2 | 68 | 0.67 | 0.94 | 31 | empty |
| 3 | 95 | 0.51 | 0.83 | 19 | empty |
| 4 | 172 | 0.44 | 0.74 | 31 | GOL |
| 5 | 72 | 0.32 | 0.74 | 14 | empty |
Interfaces
3 interfaces between chains.
- B–C · 2203 Ų buried · 56 hydrogen bonds · protein-protein
- A–B · 2202 Ų buried · 55 hydrogen bonds · protein-protein
- A–C · 2194 Ų buried · 56 hydrogen bonds · protein-protein
Compared structures
- 2WN3 · Crystal structure of Discoidin I from Dictyostelium discoideum in complex with the… · the same entry in another collection · chain A against A, TM-score 1.00
- P02886 · AlphaFold monomer V2.0 prediction for discoidin-1 subunit a (P02886) · a predicted model of the same protein · chain B against A, TM-score 0.78
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 P02886
- Elsewhere: RCSB PDB 2WN3 · PDBe 2WN3 · UniProt P02886
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