MolNFT v1 · #30756 · protein
2.6 ångström crystal structure of the complex between the nuclear snorna decapping nudix hydrolase X29 and manganese in the presence of 7-methyl-GDP
2A8Q · U8 snorna-binding protein X29: “2.6 ångström crystal structure of the complex between the nuclear snorna decapping nudix hydrolase X29 and…”. X-ray diffraction, 2 ligands (POP, MN), 4 pockets (best druggability 0.73). MolNFT v1…
- PDB
- 2A8Q
- Type
- protein
- Length
- 381 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
- POP, MN
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | U8 snorna-binding protein X29 (EC 3.6.1.-) | protein | 190 | 33% helix, 32% strand | Q569R2 |
| B | U8 snorna-binding protein X29 (EC 3.6.1.-) | protein | 191 | 33% helix, 32% strand | Q569R2 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 74 | 0.73 | 0.97 | 21 | empty |
| 2 | 219 | 0.50 | 0.76 | 33 | MN |
| 3 | 199 | 0.50 | 0.76 | 34 | MN, POP |
| 4 | 64 | 0.29 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1390 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (alkylation).
Compared structures
- 2A8Q · 2.6 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 2A8Q · PDBe 2A8Q · UniProt Q569R2
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