MolNFT v1 · #138046 · protein
Crystal structure of the HSNUDT16 in complex with MG+2 and ADP-ribose
5W6X · U8 snorna-decapping enzyme: “Crystal structure of the HSNUDT16 in complex with MG+2 and ADP-ribose”. X-ray diffraction, 2 ligands (APR, MG), 3 pockets (best druggability 0.75). MolNFT v1 #138046 on GenesisL1: 3D structure, binding…
- PDB
- 5W6X
- Type
- protein
- Length
- 353 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- U8 snorna-decapping enzyme
- EC
- 3.6.1.62, 3.6.1.64
- UniProt
- Q96DE0
- Ligands
- APR, MG
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | U8 snorna-decapping enzyme (EC 3.6.1.62, 3.6.1.64) | protein | 179 | 30% helix, 34% strand | Q96DE0 |
| B | U8 snorna-decapping enzyme (EC 3.6.1.62, 3.6.1.64) | protein | 174 | 31% helix, 34% strand | Q96DE0 |
Ligands and binding sites
- APR · Adenosine-5-diphosphoribose · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- ACY · Acetic acid · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains 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 | 82 | 0.75 | 0.98 | 26 | empty |
| 2 | 241 | 0.58 | 0.79 | 30 | APR, MG |
| 3 | 253 | 0.55 | 0.77 | 38 | APR, MG |
Interfaces
1 interface between chains.
- A–B · 1345 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5W6X · Crystal structure of the HsNUDT16 in complex with Mg+2 and ADP-ribose · the same entry in another collection · chain A against A, TM-score 1.00
- Q96DE0 · AlphaFold monomer V2.0 prediction for U8 snorna-decapping enzyme (Q96DE0) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q96DE0
- Elsewhere: RCSB PDB 5W6X · PDBe 5W6X · UniProt Q96DE0
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