MolNFT v1 · #125003 · protein + DNA
Crystal structure of the two tandem rrm domains of PUF60 bound to a portion of an adml pre-mRNA 3' splice site analog
5KVY · POLY(U)-binding-splicing factor PUF60: “Crystal structure of the two tandem rrm domains of PUF60 bound to a portion of an adml pre-mRNA 3' splice…”. X-ray diffraction, 1 ligand (CL), 3 pockets (best druggability 0.72). MolNFT v1…
- PDB
- 5KVY
- Type
- protein + DNA
- Length
- 394 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- POLY(U)-binding-splicing factor PUF60; DNA (30-mer)
- UniProt
- Q9UHX1
- Ligands
- CL
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | POLY(U)-binding-splicing factor PUF60 | protein | 195 | 32% helix, 29% strand | Q9UHX1 |
| B | POLY(U)-binding-splicing factor PUF60 | protein | 195 | 32% helix, 29% strand | Q9UHX1 |
| C | DNA (30-mer) | dna | 4 | — | — |
Ligands and binding sites
- CL · Chloride ion · ion · 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 | 1032 | 0.72 | 0.76 | 88 | empty |
| 2 | 98 | 0.34 | 0.73 | 22 | empty |
| 3 | 95 | 0.34 | 0.73 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 581 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 400 Ų buried · 8 hydrogen bonds · protein-nucleic
- B–C · 377 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 5KVY · Crystal structure of the two tandem rrm domains of PUF60 bound to a portion of an adml… · the same entry in another collection · chain C against C, 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 0.96
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 Q9UHX1
- Elsewhere: RCSB PDB 5KVY · PDBe 5KVY · UniProt Q9UHX1
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