MolNFT v1 · #168894 · protein
Crystal structure of mouse dxo in complex with 3'-fadp
6WUF · Decapping and exoribonuclease protein: “Crystal structure of mouse dxo in complex with 3'-fadp”. X-ray diffraction, 1 ligand (UBG), 3 pockets (best druggability 0.77). MolNFT v1 #168894 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6WUF
- Type
- protein
- Length
- 358 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Decapping and exoribonuclease protein
- EC
- 3.1.13.-, 3.6.1.-
- UniProt
- O70348
- Ligands
- UBG
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Decapping and exoribonuclease protein (EC 3.1.13.-, 3.6.1.-) | protein | 358 | 31% helix, 28% strand | O70348 |
Ligands and binding sites
- UBG · [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]methyl (2R,3S,4S)-5-(7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)-2,3,4-trihydroxypentyl dihydrogen diphosphate (non-preferred name) · ligand · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1117 | 0.77 | 0.79 | 69 | UBG |
| 2 | 76 | 0.32 | 0.74 | 17 | empty |
| 3 | 52 | 0.30 | 0.76 | 11 | empty |
Compared structures
- 6WUF · Crystal structure of mouse DXO in complex with 3'-FADP · the same entry in another collection · chain A against A, TM-score 1.00
- O70348 · AlphaFold monomer V2.0 prediction for decapping and exoribonuclease protein (O70348) · a predicted model of the same protein · 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 O70348
- Elsewhere: RCSB PDB 6WUF · PDBe 6WUF · UniProt O70348
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