Research workbench
Crystal structure of xerh site-specific recombinase bound to palindromic difh substrate: post-cleavage complex
Analyse Crystal structure of xerh site-specific recombinase bound to palindromic difh… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JJV
- Type
- protein + DNA
- Length
- 768 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine recombinase xerh; DNA (5'-D(*TP*AP*GP*TP*TP*AP*TP*GP*AP*AP*AP*AP*C)-3'); DNA…
- UniProt
- O25386
- Ligands
- CL
- Pockets
- 16 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 59% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine recombinase xerh | protein | 353 | 59% helix, 6% strand | O25386 |
| B | Tyrosine recombinase xerh | protein | 356 | 59% helix, 6% strand | O25386 |
| C | DNA (5'-D(*TP*AP*GP*TP*TP*AP*TP*GP*AP*AP*AP*AP*C)-3') | dna | 12 | — | — |
| D, F | DNA (5'- D(*TP*GP*CP*AP*GP*TP*TP*TP*TP*CP*AP*TP*AP*AP*CP*TP*A)-3') | dna | 17 | — | — |
| E | DNA (5'-D(*TP*AP*GP*TP*TP*AP*TP*GP*AP*AP*AP*AP*C)-3') | dna | 13 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 688 | 0.80 | 0.85 | 56 | empty |
| 2 | 85 | 0.74 | 0.97 | 21 | empty |
| 3 | 578 | 0.73 | 0.81 | 51 | empty |
| 4 | 101 | 0.70 | 0.93 | 24 | empty |
| 5 | 353 | 0.69 | 0.83 | 28 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1998 Ų buried · 22 hydrogen bonds · protein-protein
- A–E · 1230 Ų buried · 35 hydrogen bonds · protein-nucleic
- B–C · 1175 Ų buried · 34 hydrogen bonds · protein-nucleic
- A–F · 1152 Ų buried · 23 hydrogen bonds · protein-nucleic
- B–D · 1067 Ų buried · 22 hydrogen bonds · protein-nucleic
Compared structures
- 5JJV · Crystal structure of XerH site-specific recombinase bound to palindromic difH substrate… · the same entry in another collection · chain F against F, TM-score 1.00
- O25386 · AlphaFold monomer V2.0 prediction for tyrosine recombinase xerh (O25386) · a predicted model of the same protein · chain B 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 5JJV · PDBe 5JJV · UniProt O25386
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