MolNFT v1 · #174186 · protein
Crystal structure of parb from myxococcus xanthus bound to cdp and monothiophosphate
7BNK · Parb family protein: “Crystal structure of parb from myxococcus xanthus bound to cdp and monothiophosphate”. X-ray diffraction, 3 ligands (TS6, CDP, MG), 4 pockets (best druggability 0.85). MolNFT v1 #174186 on GenesisL1: 3D…
- 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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