Research workbench
Structure of the discoidin I from dictyostelium discoideum in complex with galactose beta 1-3 galnac at 1.8 a resolution.
Analyse Structure of the 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
- 2WN2
- 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, NGA, GAL, A2G, CA, SO4
- Pockets
- 6 · best druggability 0.76
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 | 252 | 5% helix, 52% strand | P02886 |
| C | Discoidin-1 subunit a | protein | 253 | 5% helix, 52% strand | P02886 |
Ligands and binding sites
- 1PG · 2-(2-{2-[2-(2-methoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethanol · ligand · chains A, C
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · 3 copies · chains A, B, C
- GAL · beta-D-galactopyranose · sugar · 3 copies · chains A, B, C
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · 3 copies · chains A, B, C
- CA · Calcium ion · metal · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · chains A, B, C
- GOL · Glycerol · additive · 8 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 229 | 0.76 | 0.90 | 52 | empty |
| 2 | 56 | 0.68 | 0.96 | 25 | empty |
| 3 | 83 | 0.55 | 0.86 | 20 | empty |
| 4 | 155 | 0.43 | 0.75 | 35 | GOL |
| 5 | 135 | 0.41 | 0.75 | 24 | GOL |
Interfaces
3 interfaces between chains.
- A–C · 2224 Ų buried · 54 hydrogen bonds · protein-protein
- B–C · 2203 Ų buried · 56 hydrogen bonds · protein-protein
- A–B · 2198 Ų buried · 55 hydrogen bonds · protein-protein
Compared structures
- 2WN2 · Structure of the discoidin I from Dictyostelium discoideum in complex with galactose beta… · 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 2WN2 · PDBe 2WN2 · UniProt P02886
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