MolNFT v1 · #127649 · protein + DNA
Mobm relaxase domain (mobv; MOB_PRE) bound to 26NT PMV158 orit DNA
5N2Q · Plasmid recombination enzyme: “Mobm relaxase domain (mobv; MOB_PRE) bound to 26NT PMV158 orit DNA”. X-ray diffraction, 3 ligands (MG, NA, CL), 2 pockets (best druggability 0.67). MolNFT v1 #127649 on GenesisL1: 3D structure, binding…
- PDB
- 5N2Q
- Type
- protein + DNA
- Length
- 200 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plasmid recombination enzyme; DNA (26-mer)
- UniProt
- P13925
- Ligands
- MG, NA, CL
- Pockets
- 2 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Plasmid recombination enzyme | protein | 174 | 41% helix, 20% strand | P13925 |
| B | DNA (26-mer) | dna | 26 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A
- NA · Sodium ion · metal · chains B
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 141 | 0.67 | 0.88 | 19 | empty |
| 2 | 190 | 0.48 | 0.76 | 21 | GOL |
Interfaces
1 interface between chains.
- A–B · 1676 Ų buried · 44 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 7 modified (engineered).
Compared structures
- 5N2Q · MobM Relaxase Domain (MOBV; Mob_Pre) bound to 26nt pMV158 oriT DNA · the same entry in another collection · chain A against A, TM-score 1.00
- P13925 · AlphaFold monomer V2.0 prediction for plasmid recombination enzyme (P13925) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P13925
- Elsewhere: RCSB PDB 5N2Q · PDBe 5N2Q · UniProt P13925
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.