Research workbench
Crystal structure of the parb-like protein padc
Analyse Crystal structure of the parb-like protein padc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RYK
- Type
- protein
- Length
- 265 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Parb-like nuclease domain protein
- UniProt
- Q1D3H3
- Ligands
- CTP, MG
- Pockets
- 3 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Parb-like nuclease domain protein | protein | 133 | 43% helix, 19% strand | Q1D3H3 |
| B | Parb-like nuclease domain protein | protein | 132 | 46% helix, 19% strand | Q1D3H3 |
Ligands and binding sites
- CTP · Cytidine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1051 | 0.85 | 0.86 | 90 | MG, CTP, GOL |
| 2 | 80 | 0.31 | 0.73 | 17 | empty |
| 3 | 74 | 0.28 | 0.72 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1830 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 6RYK · Crystal structure of the ParB-like protein PadC · 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 Q1D3H3
- Elsewhere: RCSB PDB 6RYK · PDBe 6RYK · UniProt Q1D3H3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.