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Structure of the complex of discoidin II from dictyostelium discoideum with beta-methyl-galactose
Analyse Structure of the complex of discoidin II from dictyostelium discoideum with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VMD
- Type
- protein
- Length
- 252 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Discoidin-2
- UniProt
- P42530
- Ligands
- 1PG, MBG, CA, CL
- Pockets
- 1 · best druggability 0.27
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Discoidin-2 | protein | 252 | 4% helix, 50% strand | P42530 |
Ligands and binding sites
- 1PG · 2-(2-{2-[2-(2-methoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethanol · ligand · 2 copies · chains A
- MBG · methyl beta-D-galactopyranoside · ligand · chains A
- CA · Calcium ion · metal · chains A
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 56 | 0.27 | 0.73 | 15 | empty |
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 P42530
- Elsewhere: RCSB PDB 2VMD · PDBe 2VMD · UniProt P42530
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