Research workbench
Crystal structure of PUF60 uhm domain in complex with 7,8 dimethoxyperphenazine
Analyse Crystal structure of PUF60 uhm domain in complex with 7,8 dimethoxyperphenazine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SLO
- Type
- protein
- Length
- 846 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- THIOREDOXIN,POLY(U)-binding-splicing factor PUF60
- UniProt
- A0A064CXU8, Q9UHX1
- Ligands
- LJT, MG
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | THIOREDOXIN,POLY(U)-binding-splicing factor PUF60 | protein | 214 | 31% helix, 29% strand | A0A064CXU8, Q9UHX1 |
| C, D | THIOREDOXIN,POLY(U)-binding-splicing factor PUF60 | protein | 209 | 31% helix, 30% strand | A0A064CXU8, Q9UHX1 |
Ligands and binding sites
- LJT · 2-[4-[3-(8-chloranyl-2,3-dimethoxy-phenothiazin-10-yl) propyl]piperazin-1-yl]ethanol · ligand · 2 copies · chains C, D
- MG · Magnesium ion · metal · 2 copies · chains A, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1173 | 0.77 | 0.79 | 149 | empty |
| 2 | 252 | 0.54 | 0.76 | 43 | empty |
| 3 | 134 | 0.50 | 0.79 | 21 | empty |
| 4 | 271 | 0.48 | 0.73 | 28 | empty |
| 5 | 82 | 0.44 | 0.80 | 14 | LJT |
Interfaces
6 interfaces between chains.
- B–C · 1474 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 1273 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 760 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 689 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 292 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6SLO · Crystal structure of PUF60 UHM domain in complex with 7,8 dimethoxyperphenazine · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UHX1 · AlphaFold monomer V2.0 prediction for POLY(U)-binding-splicing factor PUF60 (Q9UHX1) · a predicted model of the same protein · chain A against A, TM-score 0.51
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 A0A064CXU8
- Every structure of UniProt Q9UHX1
- Elsewhere: RCSB PDB 6SLO · PDBe 6SLO · UniProt A0A064CXU8 · UniProt Q9UHX1
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