Research workbench
The X-ray structure of a RNA-binding protein complex
Analyse The X-ray structure of a RNA-binding protein complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WNL
- Type
- protein
- Length
- 930 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SWI5-dependent ho expression protein 2; SWI5-dependent ho expression protein 3
- UniProt
- P36068, B5VE90
- Ligands
- SO4
- Pockets
- 10 · best druggability 0.69
Structure
x-ray diffraction · 6 distinct chains · 72% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | SWI5-dependent ho expression protein 2 | protein | 231 | 72% helix, 2% strand | P36068 |
| A | SWI5-dependent ho expression protein 2 | protein | 227 | 72% helix, 1% strand | P36068 |
| B | SWI5-dependent ho expression protein 2 | protein | 222 | 75% helix, 1% strand | P36068 |
| D | SWI5-dependent ho expression protein 2 | protein | 220 | 75% helix, 1% strand | P36068 |
| E, F, G | SWI5-dependent ho expression protein 3 | protein | 8 | 0% helix, 13% strand | B5VE90 |
| H | SWI5-dependent ho expression protein 3 | protein | 6 | 0% helix, 17% strand | B5VE90 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, D, B
- GOL · Glycerol · additive · 6 copies · chains C, B, D
- IPA · Isopropyl alcohol · additive · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 485 | 0.69 | 0.80 | 52 | empty |
| 2 | 390 | 0.66 | 0.79 | 43 | SO4 |
| 3 | 240 | 0.61 | 0.80 | 27 | empty |
| 4 | 152 | 0.54 | 0.80 | 17 | empty |
| 5 | 112 | 0.51 | 0.81 | 19 | empty |
Interfaces
10 interfaces between chains.
- C–B · 2016 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 1994 Ų buried · 29 hydrogen bonds · protein-protein
- D–E · 529 Ų buried · 4 hydrogen bonds · protein-protein
- B–G · 482 Ų buried · 6 hydrogen bonds · protein-protein
- C–F · 469 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4WNL · The X-ray structure of a RNA-binding protein complex · the same entry in another collection · chain H against H, TM-score 1.00
- P36068 · AlphaFold monomer V2.0 prediction for SWI5-dependent ho expression protein 2 (P36068) · a predicted model of the same protein · chain D 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 P36068
- Every structure of UniProt B5VE90
- Elsewhere: RCSB PDB 4WNL · PDBe 4WNL · UniProt P36068 · UniProt B5VE90
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.