Research workbench
Structure of the recombination mediator protein recf-ATP in recfor pathway
Analyse Structure of the recombination mediator protein recf-ATP in recfor pathway in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Z68
- Type
- protein
- Length
- 1,472 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA replication and repair protein recf
- UniProt
- Q8RDL3
- Ligands
- ATP, MG
- Pockets
- 12 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA replication and repair protein recf | protein | 368 | 43% helix, 22% strand | Q8RDL3 |
| B | DNA replication and repair protein recf | protein | 368 | 45% helix, 21% strand | Q8RDL3 |
| C | DNA replication and repair protein recf | protein | 373 | 38% helix, 22% strand | Q8RDL3 |
| D | DNA replication and repair protein recf | protein | 363 | 41% helix, 22% strand | Q8RDL3 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- IMD · Imidazole · additive · 21 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1067 | 0.85 | 0.85 | 122 | ATP, IMD, MG |
| 2 | 1143 | 0.85 | 0.85 | 118 | ATP, IMD, MG |
| 3 | 614 | 0.78 | 0.84 | 66 | ATP, IMD, MG |
| 4 | 361 | 0.69 | 0.82 | 44 | ATP, MG |
| 5 | 157 | 0.64 | 0.86 | 24 | IMD |
Interfaces
4 interfaces between chains.
- A–B · 792 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 780 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 228 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 69 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5Z68 · Structure of the recombination mediator protein RecF-ATP in RecFOR pathway · the same entry in another collection · chain D against D, 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 5Z68 · PDBe 5Z68 · UniProt Q8RDL3
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