MolNFT v1 · #149830 · protein
Crystal structure of the C. themophilum scavenger decapping enzyme dcps apo form
6GBS · Putative mRNA decapping protein: “Crystal structure of the C. themophilum scavenger decapping enzyme dcps apo form”. X-ray diffraction, 8 pockets (best druggability 0.82). MolNFT v1 #149830 on GenesisL1: 3D structure, binding sites…
- 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
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