MolNFT v1 · #99171 · protein + DNA
Mobm relaxase domain (mobv; MOB_PRE) bound to plasmid PMV158 orit DNA (22NT+3'THIOPHOSPHATE). mn-bound crystal structure at pH 6.8
4LVL · Plasmid recombination enzyme: “Mobm relaxase domain (mobv; MOB_PRE) bound to plasmid PMV158 orit DNA (22NT+3'THIOPHOSPHATE). mn-bound…”. X-ray diffraction, 3 ligands (TS6, MN, CL), 2 pockets (best druggability 0.67). MolNFT v1…
- PDB
- 4LVL
- Type
- protein + DNA
- Length
- 218 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plasmid recombination enzyme; DNA (5'-D(*AP*CP*TP*TP*TP*AP*T)-3'); DNA (5'…
- UniProt
- P13925
- Ligands
- TS6, MN, CL
- Pockets
- 2 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Plasmid recombination enzyme | protein | 196 | 42% helix, 18% strand | P13925 |
| B | DNA (5'-D(*AP*CP*TP*TP*TP*AP*T)-3') | dna | 7 | — | — |
| C | DNA (5'- D(*AP*TP*AP*AP*AP*GP*TP*AP*TP*AP*GP*TP*GP*TP*GP*(TS6))-3') | dna | 15 | — | — |
Ligands and binding sites
- TS6 · Monothiophosphate · ligand · chains A, C
- MN · Manganese (II) ion · metal · chains A, C
- CL · Chloride ion · ion · 3 copies · chains A
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 | 116 | 0.67 | 0.90 | 19 | empty |
| 2 | 159 | 0.45 | 0.76 | 21 | TS6 |
Interfaces
3 interfaces between chains.
- A–C · 1764 Ų buried · 50 hydrogen bonds · protein-nucleic
- A–B · 335 Ų buried · 5 hydrogen bonds · protein-nucleic
- B–C · 303 Ų buried · 24 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4LVL · MobM Relaxase Domain (MOBV; Mob_Pre) bound to plasmid 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 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 4LVL · PDBe 4LVL · UniProt P13925
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