Research workbench
'crystal structure of the drosophila melanogaster SNF/U2A'/U2-SL4 complex
Analyse 'crystal structure of the drosophila melanogaster SNF/U2A'/U2-SL4 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6F4G
- Type
- protein + RNA
- Length
- 586 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable U2 small nuclear ribonucleoprotein a'; U1 small nuclear ribonucleoprotein a…
- UniProt
- Q9V4Q8, P43332
- Ligands
- CL, SO4
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 5 distinct chains · 29% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable U2 small nuclear ribonucleoprotein a' | protein | 175 | 30% helix, 15% strand | Q9V4Q8 |
| B | U1 small nuclear ribonucleoprotein a | protein | 95 | 27% helix, 24% strand | P43332 |
| C, F | U2-SL4 | rna | 25 | — | — |
| D | Probable U2 small nuclear ribonucleoprotein a' | protein | 176 | 31% helix, 15% strand | Q9V4Q8 |
| E | U1 small nuclear ribonucleoprotein a | protein | 90 | 26% helix, 26% strand | P43332 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 688 | 0.67 | 0.76 | 74 | CL |
| 2 | 474 | 0.59 | 0.75 | 36 | empty |
| 3 | 178 | 0.54 | 0.79 | 32 | empty |
Interfaces
7 interfaces between chains.
- E–F · 1108 Ų buried · 37 hydrogen bonds · protein-nucleic
- B–C · 1108 Ų buried · 40 hydrogen bonds · protein-nucleic
- A–B · 946 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 892 Ų buried · 11 hydrogen bonds · protein-protein
- C–F · 311 Ų buried · 16 hydrogen bonds · nucleic-nucleic
Compared structures
- 6F4G · 'Crystal structure of the Drosophila melanogaster SNF/U2A'/U2-SL4 complex · the same entry in another collection · chain F against F, TM-score 1.00
- Q9V4Q8 · AlphaFold monomer V2.0 prediction for probable U2 small nuclear ribonucleoprotein a'… · a predicted model of the same protein · chain D against A, TM-score 0.99
- 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 Q9V4Q8
- Every structure of UniProt P43332
- Elsewhere: RCSB PDB 6F4G · PDBe 6F4G · UniProt Q9V4Q8 · UniProt P43332
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