MolNFT v1 · #103560 · protein + RNA
U1-70K in complex with U1 snrna stem-loops 1 and U1-a rrm in complex with stem-loop 2
4PKD · U1 snrna stem-loops 1 and 2 (55-mer): “U1-70K in complex with U1 snrna stem-loops 1 and U1-a rrm in complex with stem-loop 2”. X-ray diffraction, 1 ligand (MG), 4 pockets (best druggability 0.69). MolNFT v1 #103560 on GenesisL1: 3D…
- PDB
- 4PKD
- Type
- protein + RNA
- Length
- 295 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- U1 snrna stem-loops 1 and 2 (55-mer); U1 small nuclear ribonucleoprotein A,U1 small…
- UniProt
- Q06AA4, P08621
- Ligands
- MG
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| V | U1 snrna stem-loops 1 and 2 (55-mer) | rna | 55 | — | — |
| B | U1 small nuclear ribonucleoprotein A,U1 small nuclear ribonucleoprotein 70 kda | protein | 240 | 35% helix, 22% strand | Q06AA4, P08621 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 695 | 0.69 | 0.77 | 40 | empty |
| 2 | 363 | 0.60 | 0.78 | 30 | MG |
| 3 | 52 | 0.35 | 0.79 | 12 | empty |
| 4 | 56 | 0.28 | 0.75 | 12 | empty |
Interfaces
1 interface between chains.
- V–B · 2951 Ų buried · 82 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4PKD · U1-70k in complex with U1 snRNA stem-loops 1 and U1-A RRM in complex with stem-loop 2 · the same entry in another collection · chain V against V, TM-score 1.00
- P08621 · AlphaFold monomer V2.0 prediction for U1 small nuclear ribonucleoprotein 70 kda (P08621) · a predicted model of the same protein · chain B against A, TM-score 0.60
- Q06AA4 · AlphaFold monomer V2.0 prediction for U1 small nuclear ribonucleoprotein a (Q06AA4) · a predicted model of the same protein · chain B against A, TM-score 0.41
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 Q06AA4
- Every structure of UniProt P08621
- Elsewhere: RCSB PDB 4PKD · PDBe 4PKD · UniProt Q06AA4 · UniProt P08621
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