Research workbench
Crystal structure of xera recombinase
Analyse Crystal structure of xera recombinase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HXY
- Type
- protein
- Length
- 1,654 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine recombinase xera
- UniProt
- Q9HIM5
- Ligands
- PO4
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 61% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Tyrosine recombinase xera | protein | 280 | 59% helix, 5% strand | Q9HIM5 |
| B | Tyrosine recombinase xera | protein | 275 | 62% helix, 5% strand | Q9HIM5 |
| C | Tyrosine recombinase xera | protein | 277 | 62% helix, 4% strand | Q9HIM5 |
| D | Tyrosine recombinase xera | protein | 274 | 61% helix, 5% strand | Q9HIM5 |
| F | Tyrosine recombinase xera | protein | 268 | 63% helix, 4% strand | Q9HIM5 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 15 copies · chains A, F, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 606 | 0.77 | 0.84 | 65 | empty |
| 2 | 556 | 0.76 | 0.83 | 62 | empty |
| 3 | 427 | 0.72 | 0.83 | 47 | empty |
| 4 | 294 | 0.72 | 0.85 | 29 | empty |
| 5 | 268 | 0.70 | 0.85 | 28 | empty |
Interfaces
14 interfaces between chains.
- A–D · 1992 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 1971 Ų buried · 33 hydrogen bonds · protein-protein
- C–E · 1919 Ų buried · 32 hydrogen bonds · protein-protein
- D–F · 1848 Ų buried · 29 hydrogen bonds · protein-protein
- B–E · 1830 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 54 modified (engineered).
Compared structures
- 5HXY · Crystal structure of XerA recombinase · 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 Q9HIM5
- Elsewhere: RCSB PDB 5HXY · PDBe 5HXY · UniProt Q9HIM5
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