MolNFT v1 · #99172 · protein + DNA
Mobm relaxase domain (mobv; MOB_PRE) bound to plasmid PMV158 orit DNA (23NT). mn-bound crystal structure at pH 6.5
4LVM · Plasmid recombination enzyme: “Mobm relaxase domain (mobv; MOB_PRE) bound to plasmid PMV158 orit DNA (23NT). mn-bound crystal structure at…”. X-ray diffraction, 4 ligands (MN, MG, NA), 6 pockets (best druggability 0.72). MolNFT v1…
- PDB
- 4LVM
- Type
- protein + DNA
- Length
- 425 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plasmid recombination enzyme; Actttat oligonucleotide; Ataaagtatagtgtgt oligonucleotide
- UniProt
- P13925
- Ligands
- MN, MG, NA, CL
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 5 distinct chains · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Plasmid recombination enzyme | protein | 192 | 39% helix, 19% strand | P13925 |
| B, D | Actttat oligonucleotide | dna | 7 | — | — |
| E | Ataaagtatagtgtgt oligonucleotide | dna | 15 | — | — |
| C | Plasmid recombination enzyme | protein | 191 | 37% helix, 18% strand | P13925 |
| F | Ataaagtatagtgtgt oligonucleotide | dna | 13 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, E, C
- MG · Magnesium ion · metal · chains A
- NA · Sodium ion · metal · chains A, E, C
- CL · Chloride ion · ion · 5 copies · chains A, C, B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 135 | 0.72 | 0.92 | 19 | empty |
| 2 | 133 | 0.70 | 0.91 | 18 | empty |
| 3 | 643 | 0.69 | 0.77 | 70 | NA, CL |
| 4 | 414 | 0.65 | 0.79 | 33 | CL |
| 5 | 95 | 0.34 | 0.74 | 20 | empty |
Interfaces
9 interfaces between chains.
- A–E · 1812 Ų buried · 40 hydrogen bonds · protein-nucleic
- C–F · 1390 Ų buried · 29 hydrogen bonds · protein-nucleic
- A–B · 323 Ų buried · 5 hydrogen bonds · protein-nucleic
- D–F · 310 Ų buried · 28 hydrogen bonds · nucleic-nucleic
- B–E · 304 Ų buried · 26 hydrogen bonds · nucleic-nucleic
Compared structures
- 4LVM · MobM Relaxase Domain (MOBV; Mob_Pre) bound to plasmid pMV158 oriT DNA (23nt). Mn-bound… · the same entry in another collection · chain F against F, TM-score 1.00
- P13925 · AlphaFold monomer V2.0 prediction for plasmid recombination enzyme (P13925) · a predicted model of the same protein · chain C 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 4LVM · PDBe 4LVM · UniProt P13925
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.