Research workbench
Parm from R1 plasmid in complex with peptide from C-terminus of parr
Analyse Parm from R1 plasmid in complex with peptide from C-terminus of parr in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4A62
- Type
- protein
- Length
- 666 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plasmid segregation protein parm; Protein stbb
- UniProt
- P11904, P11906
- Ligands
- ANP, MG
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Plasmid segregation protein parm | protein | 320 | 39% helix, 26% strand | P11904 |
| C, D | Protein stbb | protein | 13 | 77% helix, 0% strand | P11906 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 302 | 0.76 | 0.88 | 57 | ANP, MG |
| 2 | 291 | 0.75 | 0.88 | 50 | ANP, MG |
| 3 | 624 | 0.69 | 0.77 | 56 | empty |
| 4 | 101 | 0.38 | 0.75 | 16 | empty |
| 5 | 98 | 0.37 | 0.75 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1007 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 672 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 648 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 4A62 · ParM from R1 plasmid in complex with peptide from C-terminus of ParR · the same entry in another collection · chain A against A, TM-score 1.00
- P11904 · AlphaFold monomer V2.0 prediction for plasmid segregation protein parm (P11904) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P11906 · AlphaFold monomer V2.0 prediction for protein stbb (P11906) · a predicted model of the same protein · chain C against A, TM-score 0.54
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 P11904
- Every structure of UniProt P11906
- Elsewhere: RCSB PDB 4A62 · PDBe 4A62 · UniProt P11904 · UniProt P11906
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