MolNFT v1 · #148364 · protein + RNA
Crystal structure of the drosophila melanogaster SNF/U1-SL2 complex
6F4H · U1 small nuclear ribonucleoprotein a: “Crystal structure of the drosophila melanogaster SNF/U1-SL2 complex”. X-ray diffraction, 7 pockets (best druggability 0.53). MolNFT v1 #148364 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6F4H
- Type
- protein + RNA
- Length
- 343 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- U1 small nuclear ribonucleoprotein a; U1-SL2
- UniProt
- P43332
- Pockets
- 7 · best druggability 0.53
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | U1 small nuclear ribonucleoprotein a | protein | 90 | 29% helix, 26% strand | P43332 |
| B, D, F | U1-SL2 | rna | 22 | — | — |
| C | U1 small nuclear ribonucleoprotein a | protein | 96 | 32% helix, 24% strand | P43332 |
| E | U1 small nuclear ribonucleoprotein a | protein | 91 | 32% helix, 25% strand | P43332 |
Ligands and binding sites
- FLC · Citrate anion · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 380 | 0.53 | 0.73 | 26 | empty |
| 2 | 317 | 0.51 | 0.73 | 23 | FLC |
| 3 | 293 | 0.49 | 0.74 | 21 | empty |
| 4 | 183 | 0.44 | 0.74 | 25 | empty |
| 5 | 97 | 0.33 | 0.73 | 17 | empty |
Interfaces
7 interfaces between chains.
- C–D · 1094 Ų buried · 37 hydrogen bonds · protein-nucleic
- A–B · 927 Ų buried · 33 hydrogen bonds · protein-nucleic
- E–F · 915 Ų buried · 33 hydrogen bonds · protein-nucleic
- A–C · 602 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 236 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6F4H · Crystal structure of the Drosophila melanogaster SNF/U1-SL2 complex · the same entry in another collection · chain F against F, TM-score 1.00
- P43332 · AlphaFold monomer V2.0 prediction for U1 small nuclear ribonucleoprotein a (P43332) · a predicted model of the same protein · chain E 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 P43332
- Elsewhere: RCSB PDB 6F4H · PDBe 6F4H · UniProt P43332
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