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2.1 ångström crystal structure of the complex between the nuclear U8 snorna decapping nudix hydrolase X29, manganese and M7G-ppp-a
Analyse 2.1 ångström crystal structure of the complex between the nuclear U8 snorna… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2A8T
- 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
- MGT, ADN, MN
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | U8 snorna-binding protein X29 (EC 3.6.1.-) | protein | 192 | 34% helix, 32% strand | Q569R2 |
| B | U8 snorna-binding protein X29 (EC 3.6.1.-) | protein | 191 | 34% helix, 33% strand | Q569R2 |
Ligands and binding sites
- MGT · 7N-methyl-8-hydroguanosine-5'-triphosphate · ligand · 2 copies · chains A, B
- ADN · Adenosine · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 7 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 | 72 | 0.74 | 0.98 | 19 | empty |
| 2 | 186 | 0.53 | 0.78 | 27 | MN, ADN |
| 3 | 217 | 0.53 | 0.77 | 33 | MN, ADN |
Interfaces
1 interface between chains.
- A–B · 1354 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 2A8T · 2.1 Angstrom Crystal Structure of the Complex Between the Nuclear U8 snoRNA Decapping… · the same entry in another collection · chain B against B, 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 2A8T · PDBe 2A8T · UniProt Q569R2
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