Research workbench
Native structure of the recombinant discoidin II of dictyostelium discoideum at 1.75 ångström
Analyse Native structure of the recombinant discoidin II of dictyostelium discoideum at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VM9
- 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
- CA, PO4, 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
- CA · Calcium ion · metal · chains A
- PO4 · Phosphate ion · ion · 3 copies · chains A
- CL · Chloride ion · ion · 3 copies · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · 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 | 57 | 0.27 | 0.73 | 17 | empty |
Compared structures
- 2VM9 · Native structure of the recombinant discoidin II of Dictyostelium discoideum at 1.75… · the same entry in another collection · chain A against A, TM-score 1.00
- P42530 · AlphaFold monomer V2.0 prediction for discoidin-2 (P42530) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 2VM9 · PDBe 2VM9 · UniProt P42530
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.