Research workbench
Structure of the uhm domain of PUF60 fused to thioredoxin
Analyse Structure of the uhm domain of PUF60 fused to thioredoxin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DXB
- Type
- protein
- Length
- 1,695 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thioredoxin N-terminally fused to PUF60(UHM)
- UniProt
- P0AA27, Q9UHX1
- Ligands
- CL
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thioredoxin N-terminally fused to PUF60(UHM) | protein | 214 | 30% helix, 28% strand | P0AA27, Q9UHX1 |
| B, C, F, G, H | Thioredoxin N-terminally fused to PUF60(UHM) | protein | 211 | 31% helix, 30% strand | P0AA27, Q9UHX1 |
| D | Thioredoxin N-terminally fused to PUF60(UHM) | protein | 216 | 29% helix, 27% strand | P0AA27, Q9UHX1 |
| E | Thioredoxin N-terminally fused to PUF60(UHM) | protein | 210 | 30% helix, 30% strand | P0AA27, Q9UHX1 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 973 | 0.77 | 0.80 | 91 | empty |
| 2 | 936 | 0.76 | 0.79 | 101 | empty |
| 3 | 329 | 0.63 | 0.79 | 37 | empty |
| 4 | 553 | 0.62 | 0.74 | 83 | empty |
| 5 | 238 | 0.56 | 0.78 | 36 | empty |
Interfaces
19 interfaces between chains.
- A–F · 1637 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 1534 Ų buried · 22 hydrogen bonds · protein-protein
- E–H · 1358 Ų buried · 17 hydrogen bonds · protein-protein
- C–G · 1262 Ų buried · 13 hydrogen bonds · protein-protein
- D–G · 776 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3DXB · Structure of the UHM domain of Puf60 fused to thioredoxin · the same entry in another collection · chain G against G, 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 E against A, TM-score 0.52
- P0AA27 · AlphaFold monomer V2.0 prediction for thioredoxin 1 (P0AA27) · a predicted model of the same protein · chain E against A, TM-score 0.50
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 P0AA27
- Every structure of UniProt Q9UHX1
- Elsewhere: RCSB PDB 3DXB · PDBe 3DXB · UniProt P0AA27 · UniProt Q9UHX1
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