Research workbench
Crystal structure of the C. themophilum scavenger decapping enzyme dcps apo form
Analyse Crystal structure of the C. themophilum scavenger decapping enzyme dcps apo form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GBS
- Type
- protein
- Length
- 663 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative mRNA decapping protein
- UniProt
- G0S8A3
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative mRNA decapping protein | protein | 330 | 35% helix, 28% strand | G0S8A3 |
| B | Putative mRNA decapping protein | protein | 333 | 35% helix, 28% strand | G0S8A3 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 12 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A, B
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 | 242 | 0.82 | 0.95 | 51 | empty |
| 2 | 792 | 0.71 | 0.77 | 87 | EDO |
| 3 | 257 | 0.52 | 0.75 | 26 | EDO |
| 4 | 178 | 0.47 | 0.75 | 20 | empty |
| 5 | 87 | 0.44 | 0.79 | 25 | EDO |
Interfaces
1 interface between chains.
- A–B · 4851 Ų buried · 107 hydrogen bonds · protein-protein
Compared structures
- 6GBS · Crystal Structure of the C. themophilum Scavenger Decapping Enzyme DcpS apo form · the same entry in another collection · chain A against A, TM-score 1.00
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 G0S8A3
- Elsewhere: RCSB PDB 6GBS · PDBe 6GBS · UniProt G0S8A3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.