Research workbench
Leishmania infantum RAD51 surrogate LIRADA10 in complex with 5,6,7,8- tetrahydro-2-naphthoic acid
Analyse Leishmania infantum RAD51 surrogate LIRADA10 in complex with 5,6,7,8… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TUU
- Type
- protein
- Length
- 884 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA repair and recombination protein rada
- UniProt
- O74036
- Ligands
- NY5, PO4, CL
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA repair and recombination protein rada | protein | 214 | 40% helix, 27% strand | O74036 |
| B | DNA repair and recombination protein rada | protein | 222 | 38% helix, 26% strand | O74036 |
| C | DNA repair and recombination protein rada | protein | 225 | 38% helix, 26% strand | O74036 |
| D | DNA repair and recombination protein rada | protein | 223 | 39% helix, 26% strand | O74036 |
Ligands and binding sites
- NY5 · 5,6,7,8-tetrahydronaphthalene-2-carboxylic acid · ligand · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- CL · Chloride ion · ion · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 953 | 0.83 | 0.85 | 106 | empty |
| 2 | 792 | 0.75 | 0.80 | 64 | empty |
| 3 | 262 | 0.69 | 0.85 | 54 | empty |
| 4 | 98 | 0.49 | 0.81 | 25 | empty |
| 5 | 89 | 0.49 | 0.82 | 24 | empty |
Interfaces
5 interfaces between chains.
- A–C · 842 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 521 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 449 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 319 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 268 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6TUU · Leishmania infantum Rad51 surrogate LiRadA10 in complex with… · the same entry in another collection · chain D against D, TM-score 1.00
- O74036 · AlphaFold monomer V2.0 prediction for DNA repair and recombination protein rada (O74036) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 O74036
- Elsewhere: RCSB PDB 6TUU · PDBe 6TUU · UniProt O74036
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