Research workbench
Crystal structure of parb from myxococcus xanthus bound to cdp and monothiophosphate
Analyse Crystal structure of parb from myxococcus xanthus bound to cdp and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BNK
- Type
- protein
- Length
- 387 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Parb family protein
- UniProt
- Q1CVJ4
- Ligands
- TS6, CDP, MG
- Pockets
- 4 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 56% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Parb family protein | protein | 194 | 57% helix, 12% strand | Q1CVJ4 |
| B | Parb family protein | protein | 193 | 55% helix, 12% strand | Q1CVJ4 |
Ligands and binding sites
- TS6 · Monothiophosphate · ligand · 2 copies · chains A, B
- CDP · Cytidine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 284 | 0.85 | 0.96 | 52 | TS6, CDP, MG |
| 2 | 181 | 0.48 | 0.76 | 35 | empty |
| 3 | 189 | 0.47 | 0.75 | 32 | empty |
| 4 | 63 | 0.29 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2488 Ų buried · 41 hydrogen bonds · protein-protein
Compared structures
- 7BNK · Crystal structure of ParB from Myxococcus xanthus bound to CDP and Monothiophosphate · 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 Q1CVJ4
- Elsewhere: RCSB PDB 7BNK · PDBe 7BNK · UniProt Q1CVJ4
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