Research workbench
Structure of recj complexed with DNA
Analyse Structure of recj complexed with DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5F55
- Type
- protein + DNA
- Length
- 719 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Single-stranded-DNA-specific exonuclease; DNA (5'-D(*GP*AP*TP*GP*TP*AP*CP*GP*CP*TP*AP*GP*G…
- UniProt
- D0EM60
- Ligands
- MN, SO4
- Pockets
- 10 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Single-stranded-DNA-specific exonuclease | protein | 705 | 46% helix, 18% strand | D0EM60 |
| C | DNA (5'-D(*GP*AP*TP*GP*TP*AP*CP*GP*CP*TP*AP*GP*GP*C)-3') | dna | 14 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, C
- SO4 · Sulfate ion · ion · 7 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 112 | 0.70 | 0.93 | 29 | SO4 |
| 2 | 932 | 0.68 | 0.74 | 86 | SO4 |
| 3 | 216 | 0.53 | 0.77 | 26 | empty |
| 4 | 167 | 0.49 | 0.77 | 24 | empty |
| 5 | 142 | 0.44 | 0.76 | 33 | empty |
Interfaces
1 interface between chains.
- A–C · 1519 Ų buried · 23 hydrogen bonds · protein-nucleic
Compared structures
- 5F55 · Structure of RecJ complexed with DNA · the same entry in another collection · 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 D0EM60
- Elsewhere: RCSB PDB 5F55 · PDBe 5F55 · UniProt D0EM60
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.