Research workbench
Crystal structure of mutant S. pombe RAI1 (E150S/E199Q/E239Q) in complex with 3'-fadp
Analyse Crystal structure of mutant S. pombe RAI1 (E150S/E199Q/E239Q) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WUI
- Type
- protein
- Length
- 314 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Decapping nuclease DIN1
- EC
- 3.6.1.-
- UniProt
- O13836
- Ligands
- UBG
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Decapping nuclease DIN1 (EC 3.6.1.-) | protein | 314 | 26% helix, 30% strand | O13836 |
Ligands and binding sites
- UBG · [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]methyl (2R,3S,4S)-5-(7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)-2,3,4-trihydroxypentyl dihydrogen diphosphate (non-preferred name) · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1034 | 0.76 | 0.78 | 68 | UBG |
| 2 | 53 | 0.40 | 0.81 | 12 | empty |
| 3 | 92 | 0.37 | 0.75 | 23 | empty |
Compared structures
- 6WUI · Crystal Structure of mutant S. pombe Rai1 (E150S/E199Q/E239Q) in complex with 3'-FADP · the same entry in another collection · chain A against A, TM-score 1.00
- O13836 · AlphaFold monomer V2.0 prediction for decapping nuclease DIN1 (O13836) · 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 O13836
- Elsewhere: RCSB PDB 6WUI · PDBe 6WUI · UniProt O13836
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