MolNFT v1 · #30222 · protein + DNA
Structure of parb bound to DNA
1ZX4 · Pars-small DNA centromere site: “Structure of parb bound to DNA”. X-ray diffraction, 3 pockets (best druggability 0.64). MolNFT v1 #30222 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1ZX4
- Type
- protein + DNA
- Length
- 406 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pars-small DNA centromere site; Plasmid partition par B protein
- UniProt
- Q38420
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 4 distinct chains · 61% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | Pars-small DNA centromere site | dna | 25 | — | — |
| S | Pars-small DNA centromere site | dna | 25 | — | — |
| A | Plasmid partition par B protein | protein | 180 | 63% helix, 11% strand | Q38420 |
| B | Plasmid partition par B protein | protein | 176 | 59% helix, 12% strand | Q38420 |
Ligands and binding sites
- CIT · Citric acid · additive · 2 copies · chains S, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 509 | 0.64 | 0.77 | 42 | empty |
| 2 | 232 | 0.59 | 0.80 | 48 | empty |
| 3 | 63 | 0.29 | 0.74 | 14 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1795 Ų buried · 23 hydrogen bonds · protein-protein
- T–S · 1132 Ų buried · 128 hydrogen bonds · nucleic-nucleic
- T–A · 467 Ų buried · 12 hydrogen bonds · protein-nucleic
- S–A · 334 Ų buried · 8 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 1ZX4 · Structure of ParB bound to DNA · the same entry in another collection · chain T against T, 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 Q38420
- Elsewhere: RCSB PDB 1ZX4 · PDBe 1ZX4 · UniProt Q38420
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.