Research workbench
2.45 ångström crystal structure of the complex between the nuclear snorna decapping nudix hydrolase X29, manganese and GTP
Analyse 2.45 ångström crystal structure of the complex between the nuclear snorna… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2A8S
- Type
- protein
- Length
- 383 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- U8 snorna-binding protein X29
- EC
- 3.6.1.-
- UniProt
- Q569R2
- Ligands
- GTP, MN
- Pockets
- 3 · best druggability 0.74
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 (EC 3.6.1.-) | protein | 192 | 33% helix, 32% strand | Q569R2 |
| B | U8 snorna-binding protein X29 (EC 3.6.1.-) | protein | 191 | 34% helix, 30% strand | Q569R2 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 83 | 0.74 | 0.97 | 22 | empty |
| 2 | 255 | 0.56 | 0.78 | 37 | MN, GTP |
| 3 | 216 | 0.53 | 0.77 | 32 | MN, GTP |
Interfaces
1 interface between chains.
- A–B · 1378 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (alkylation).
Compared structures
- 2A8S · 2.45 Angstrom Crystal Structure of the Complex Between the Nuclear SnoRNA Decapping Nudix… · 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 Q569R2
- Elsewhere: RCSB PDB 2A8S · PDBe 2A8S · UniProt Q569R2
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