Research workbench
Crystal structure of xenopus laevis nudix hydrolase nuclear snorna decapping protein X29
Analyse Crystal structure of xenopus laevis nudix hydrolase nuclear snorna decapping… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1U20
- Type
- protein
- Length
- 388 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- U8 snorna-binding protein X29
- UniProt
- Q6TEC1
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | U8 snorna-binding protein X29 | protein | 196 | 33% helix, 29% strand | Q6TEC1 |
| B | U8 snorna-binding protein X29 | protein | 192 | 33% helix, 32% strand | Q6TEC1 |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 69 | 0.72 | 0.97 | 18 | empty |
| 2 | 213 | 0.57 | 0.79 | 28 | empty |
| 3 | 237 | 0.53 | 0.77 | 35 | GOL |
| 4 | 53 | 0.25 | 0.73 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1390 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 1U20 · Crystal Structure of Xenopus laevis nudix hydrolase nuclear SnoRNA decapping Protein X29 · the same entry in another collection · chain A against A, TM-score 1.00
- Q6TEC1 · AlphaFold monomer V2.0 prediction for U8 snorna-decapping enzyme (Q6TEC1) · a predicted model of the same protein · chain B 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 Q6TEC1
- Elsewhere: RCSB PDB 1U20 · PDBe 1U20 · UniProt Q6TEC1
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