MolNFT v1 · #118540 · protein + DNA
Structure of recj complexed with DNA and ssb-ct
5F56 · Single-stranded-DNA-specific exonuclease: “Structure of recj complexed with DNA and ssb-ct”. X-ray diffraction, 2 ligands (MN, SO4), 9 pockets (best druggability 0.69). MolNFT v1 #118540 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5F56
- Type
- protein + DNA
- Length
- 717 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Single-stranded-DNA-specific exonuclease; DNA (5'-D(*CP*TP*GP*AP*TP*GP*GP*CP*A)-3')…
- UniProt
- D0EM60
- Ligands
- MN, SO4
- Pockets
- 9 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Single-stranded-DNA-specific exonuclease | protein | 703 | 47% helix, 18% strand | D0EM60 |
| C | DNA (5'-D(*CP*TP*GP*AP*TP*GP*GP*CP*A)-3') | dna | 9 | — | — |
| B | Ala-asp-leu-pro-phe | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, C
- SO4 · Sulfate ion · ion · 3 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 117 | 0.69 | 0.92 | 25 | SO4 |
| 2 | 459 | 0.59 | 0.75 | 49 | empty |
| 3 | 257 | 0.54 | 0.76 | 39 | empty |
| 4 | 203 | 0.47 | 0.75 | 42 | empty |
| 5 | 75 | 0.46 | 0.83 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–C · 1484 Ų buried · 30 hydrogen bonds · protein-nucleic
- A–B · 346 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5F56 · Structure of RecJ complexed with DNA and SSB-ct · 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 5F56 · PDBe 5F56 · UniProt D0EM60
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