Research workbench
Crystal structure of xerh site-specific recombinase bound to difh substrate: pre-cleavage complex
Analyse Crystal structure of xerh site-specific recombinase bound to difh substrate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JK0
- Type
- protein + DNA
- Length
- 1,508 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine recombinase xerh; DNA (30-mer)
- UniProt
- O25386
- Ligands
- CL
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 7 distinct chains · 59% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine recombinase xerh | protein | 347 | 58% helix, 7% strand | O25386 |
| B | Tyrosine recombinase xerh | protein | 345 | 59% helix, 6% strand | O25386 |
| C | Tyrosine recombinase xerh | protein | 348 | 60% helix, 7% strand | O25386 |
| D | Tyrosine recombinase xerh | protein | 349 | 58% helix, 7% strand | O25386 |
| E, G | DNA (30-mer) | dna | 30 | — | — |
| F | DNA (30-mer) | dna | 30 | — | — |
| H | DNA (30-mer) | dna | 29 | — | — |
Ligands and binding sites
- CL · Chloride ion · ion · chains A, C
- GOL · Glycerol · additive · 5 copies · chains A, B, D, C
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, C, F, D
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1088 | 0.83 | 0.84 | 112 | EDO |
| 2 | 523 | 0.77 | 0.85 | 61 | empty |
| 3 | 297 | 0.75 | 0.88 | 26 | empty |
| 4 | 287 | 0.73 | 0.87 | 24 | empty |
| 5 | 390 | 0.73 | 0.84 | 57 | empty |
Interfaces
18 interfaces between chains.
- A–C · 1787 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 1758 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1747 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 1609 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 1384 Ų buried · 98 hydrogen bonds · nucleic-nucleic
Compared structures
- 5JK0 · Crystal structure of XerH site-specific recombinase bound to difH substrate: pre-cleavage… · the same entry in another collection · chain H against H, TM-score 1.00
- O25386 · AlphaFold monomer V2.0 prediction for tyrosine recombinase xerh (O25386) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 O25386
- Elsewhere: RCSB PDB 5JK0 · PDBe 5JK0 · UniProt O25386
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