MolNFT v1 · #125826 · protein
Rada bound to dtdp
5LKM · DNA repair protein rada: “Rada bound to dtdp”. X-ray diffraction, 2 ligands (TYD, MG), 17 pockets (best druggability 0.75). MolNFT v1 #125826 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5LKM
- Type
- protein
- Length
- 1,109 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA repair protein rada
- UniProt
- A0A0T7K9X0
- Ligands
- TYD, MG
- Pockets
- 17 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA repair protein rada | protein | 390 | 32% helix, 28% strand | A0A0T7K9X0 |
| B | DNA repair protein rada | protein | 346 | 35% helix, 27% strand | A0A0T7K9X0 |
| C | DNA repair protein rada | protein | 373 | 31% helix, 28% strand | A0A0T7K9X0 |
Ligands and binding sites
- TYD · Thymidine-5'-diphosphate · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 88 | 0.75 | 0.97 | 20 | empty |
| 2 | 1111 | 0.74 | 0.77 | 80 | TYD, MG |
| 3 | 374 | 0.72 | 0.83 | 42 | empty |
| 4 | 318 | 0.68 | 0.83 | 49 | TYD, MG |
| 5 | 59 | 0.68 | 0.96 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–B · 2212 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 1543 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 5LKM · RadA bound to dTDP · 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 A0A0T7K9X0
- Elsewhere: RCSB PDB 5LKM · PDBe 5LKM · UniProt A0A0T7K9X0
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