MolNFT v1 · #138784 · protein
Crystal structure of human TUT1 bound with mgutp, form II
5WU3 · Speckle targeted PIP5K1A-regulated POLY(A) polymerase: “Crystal structure of human TUT1 bound with mgutp, form II”. X-ray diffraction, 3 ligands (UTP, MG, CL), 9 pockets (best druggability 0.72). MolNFT v1 #138784 on GenesisL1: 3D…
- PDB
- 5WU3
- Type
- protein
- Length
- 969 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Speckle targeted PIP5K1A-regulated POLY(A) polymerase
- EC
- 2.7.7.19, 2.7.7.52
- UniProt
- Q9H6E5
- Ligands
- UTP, MG, CL
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Speckle targeted PIP5K1A-regulated POLY(A) polymerase (EC 2.7.7.19, 2.7.7.52) | protein | 484 | 46% helix, 15% strand | Q9H6E5 |
| B | Speckle targeted PIP5K1A-regulated POLY(A) polymerase (EC 2.7.7.19, 2.7.7.52) | protein | 485 | 46% helix, 16% strand | Q9H6E5 |
Ligands and binding sites
- UTP · Uridine 5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 674 | 0.72 | 0.79 | 67 | UTP, MG, EDO |
| 2 | 524 | 0.70 | 0.80 | 52 | UTP, MG, EDO |
| 3 | 444 | 0.59 | 0.75 | 59 | empty |
| 4 | 273 | 0.59 | 0.79 | 41 | empty |
| 5 | 275 | 0.58 | 0.78 | 43 | empty |
Interfaces
1 interface between chains.
- A–B · 516 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5WU3 · Crystal structure of human Tut1 bound with MgUTP, form II · the same entry in another collection · chain A against A, TM-score 1.00
- Q9H6E5 · AlphaFold monomer V2.0 prediction for speckle targeted PIP5K1A-regulated POLY(A)… · a predicted model of the same protein · chain A 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 Q9H6E5
- Elsewhere: RCSB PDB 5WU3 · PDBe 5WU3 · UniProt Q9H6E5
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