MolNFT v1 · #135070 · protein
S. tokodaii xpb II crystal structure at 3.0 ångström resolution
5TNU · DNA-dependent ATPase xpbii: “S. tokodaii xpb II crystal structure at 3.0 ångström resolution”. X-ray diffraction, 2 ligands (SO4, CL), 9 pockets (best druggability 0.75). MolNFT v1 #135070 on GenesisL1: 3D structure, binding sites…
- PDB
- 5TNU
- Type
- protein
- Length
- 852 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-dependent ATPase xpbii
- UniProt
- Q970I2
- Ligands
- SO4, CL
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-dependent ATPase xpbii | protein | 441 | 44% helix, 19% strand | Q970I2 |
| B | DNA-dependent ATPase xpbii | protein | 411 | 27% helix, 16% strand | Q970I2 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 12 copies · chains A, B
- CL · Chloride ion · ion · 7 copies · chains A, B
- GOL · Glycerol · additive · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 661 | 0.75 | 0.81 | 72 | empty |
| 2 | 253 | 0.68 | 0.84 | 35 | empty |
| 3 | 545 | 0.65 | 0.76 | 52 | SO4, CL |
| 4 | 431 | 0.63 | 0.77 | 51 | SO4 |
| 5 | 409 | 0.62 | 0.77 | 51 | empty |
Interfaces
1 interface between chains.
- A–B · 604 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5TNU · S. tokodaii XPB II crystal structure at 3.0 Angstrom resolution · 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 Q970I2
- Elsewhere: RCSB PDB 5TNU · PDBe 5TNU · UniProt Q970I2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.