MolNFT v1 · #114562 · protein + RNA
Crystal structure of ashbya gossypii RAI1 in complex with PU(S)6-MN2+
5BTE · AFR263CP: “Crystal structure of ashbya gossypii RAI1 in complex with PU(S)6-MN2+”. X-ray diffraction, 2 ligands (MN, SO4), 8 pockets (best druggability 0.86). MolNFT v1 #114562 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5BTE
- Type
- protein + RNA
- Length
- 745 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AFR263CP; RNA (5'-R(P*UP*(U37)P*(U37)P*UP*UP*U)-3')
- UniProt
- Q753P9
- Ligands
- MN, SO4
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | AFR263CP | protein | 368 | 33% helix, 27% strand | Q753P9 |
| D, C | RNA (5'-R(P*UP*(U37)P*(U37)P*UP*UP*U)-3') | rna | 6 | — | — |
| A | AFR263CP | protein | 365 | 33% helix, 27% strand | Q753P9 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 6 copies · chains B, D, C, A
- SO4 · Sulfate ion · ion · 2 copies · chains B, A
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 | 996 | 0.86 | 0.87 | 111 | MN, SO4 |
| 2 | 878 | 0.84 | 0.86 | 85 | MN, SO4 |
| 3 | 200 | 0.62 | 0.82 | 35 | empty |
| 4 | 113 | 0.44 | 0.78 | 16 | empty |
| 5 | 115 | 0.40 | 0.75 | 24 | empty |
Interfaces
3 interfaces between chains.
- B–D · 780 Ų buried · 19 hydrogen bonds · protein-nucleic
- C–A · 779 Ų buried · 17 hydrogen bonds · protein-nucleic
- B–A · 545 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 5BTE · Crystal structure of Ashbya gossypii Rai1 in complex with pU(S)6-Mn2+ · the same entry in another collection · chain B against B, TM-score 1.00
- Q753P9 · AlphaFold monomer V2.0 prediction for decapping nuclease RAI1 (Q753P9) · 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 Q753P9
- Elsewhere: RCSB PDB 5BTE · PDBe 5BTE · UniProt Q753P9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.