Research workbench
MobM Relaxase Domain (MOBV; Mob_Pre) bound to plasmid pMV158 oriT DNA (22nt+3'Phosphate). Mn-bound crystal structure at pH 4.6
Analyse MobM Relaxase Domain (MOBV; Mob_Pre) bound to plasmid pMV158 oriT DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LVK
- Type
- protein + DNA
- Length
- 213 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.37
- Source
- Streptococcus agalactiae; SYNTHETIC CONSTRUCT
- Molecule
- Plasmid recombination enzyme; ACTTTAT oligonucleotide; ATAAAGTATAGTGTGpo oligonucleotide
- UniProt
- P13925
- Ligands
- MN, NA
- Pockets
- 2 · best druggability 0.69
Structure
x-ray diffraction · resolution 2.37 · 3 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Plasmid recombination enzyme | protein | 191 | 43% helix, 18% strand | P13925 |
| B | ACTTTAT oligonucleotide | dna | 7 | — | — |
| C | ATAAAGTATAGTGTGpo oligonucleotide | dna | 15 | — | — |
Ligands and binding sites
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 | 125 | 0.69 | 0.90 | 19 | empty |
| 2 | 195 | 0.49 | 0.77 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1750 Ų buried · 42 hydrogen bonds · protein-nucleic
- A–B · 319 Ų buried · 6 hydrogen bonds · protein-nucleic
- B–C · 301 Ų buried · 26 hydrogen bonds · nucleic-nucleic
Compared structures
- 4LVK · Mobm relaxase domain (mobv; MOB_PRE) bound to plasmid PMV158 orit DNA (22NT+3'PHOSPHATE).… · 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 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 P13925
- Elsewhere: RCSB PDB 4LVK · PDBe 4LVK · UniProt P13925
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