Research workbench
Mechanism of homologous recombination from the reca-SSDNA/DSDNA structures
Analyse Mechanism of homologous recombination from the reca-SSDNA/DSDNA structures in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CMW
- Type
- protein + DNA
- Length
- 3,241 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DT)-3'); Protein reca
- UniProt
- P0A7G6
- Ligands
- ALF, ADP, MG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D | DNA (5'- D(*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DT)-3') | dna | 12 | — | — |
| A | Protein reca | protein | 1609 | 40% helix, 26% strand | P0A7G6 |
| C | Protein reca | protein | 1608 | 40% helix, 26% strand | P0A7G6 |
Ligands and binding sites
- ALF · Tetrafluoroaluminate ion · ligand · 10 copies · chains A, C
- ADP · Adenosine-5'-diphosphate · ligand · 10 copies · chains A, C
- MG · Magnesium ion · metal · 10 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 925 | 0.83 | 0.85 | 95 | MG, ALF, ADP |
| 2 | 275 | 0.79 | 0.91 | 40 | MG, ALF, ADP |
| 3 | 627 | 0.79 | 0.84 | 76 | MG, ALF, ADP |
| 4 | 528 | 0.78 | 0.85 | 61 | MG, ALF, ADP |
| 5 | 559 | 0.78 | 0.84 | 67 | MG, ALF, ADP |
Interfaces
5 interfaces between chains.
- A–C · 2514 Ų buried · 21 hydrogen bonds · protein-protein
- B–A · 2266 Ų buried · 37 hydrogen bonds · protein-nucleic
- D–C · 2215 Ų buried · 34 hydrogen bonds · protein-nucleic
- D–A · 66 Ų buried · 0 hydrogen bonds · protein-nucleic
- B–C · 49 Ų buried · 0 hydrogen bonds · protein-nucleic
Compared structures
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 P0A7G6
- Elsewhere: RCSB PDB 3CMW · PDBe 3CMW · UniProt P0A7G6
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