MolNFT v1 · #141400 · protein
Structure of the recombination mediator protein recf-atprs in recfor pathway
5Z69 · DNA replication and repair protein recf: “Structure of the recombination mediator protein recf-atprs in recfor pathway”. X-ray diffraction, 1 ligand (AGS), 9 pockets (best druggability 0.78). MolNFT v1 #141400 on GenesisL1: 3D…
- PDB
- 5Z69
- Type
- protein
- Length
- 743 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA replication and repair protein recf
- UniProt
- Q8RDL3
- Ligands
- AGS
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA replication and repair protein recf | protein | 372 | 44% helix, 23% strand | Q8RDL3 |
| B | DNA replication and repair protein recf | protein | 371 | 47% helix, 23% strand | Q8RDL3 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 670 | 0.78 | 0.83 | 86 | empty |
| 2 | 170 | 0.69 | 0.88 | 33 | empty |
| 3 | 276 | 0.67 | 0.82 | 30 | empty |
| 4 | 383 | 0.66 | 0.79 | 32 | empty |
| 5 | 207 | 0.58 | 0.80 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 976 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5Z69 · Structure of the recombination mediator protein RecF-ATPrS in RecFOR pathway · the same entry in another collection · chain A against A, TM-score 1.00
- Q8RDL3 · AlphaFold monomer V2.0 prediction for DNA replication and repair protein recf (Q8RDL3) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q8RDL3
- Elsewhere: RCSB PDB 5Z69 · PDBe 5Z69 · UniProt Q8RDL3
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