Research workbench
Crystal structure of human YBX2 csd in complex with M5C RNA in space group P1
Analyse Crystal structure of human YBX2 csd in complex with M5C RNA in space group P1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7F3J
- Type
- protein + RNA
- Length
- 378 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Y-box-binding protein 2; RNA (5'-R(*UP*CP*AP*UP*(5MC))-3')
- UniProt
- Q9Y2T7
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Y-box-binding protein 2 | protein | 89 | 7% helix, 48% strand | Q9Y2T7 |
| B, D, F, H | RNA (5'-R(*UP*CP*AP*UP*(5MC))-3') | rna | 5 | — | — |
| E, G | Y-box-binding protein 2 | protein | 90 | 7% helix, 50% strand | Q9Y2T7 |
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 | 799 | 0.69 | 0.76 | 80 | empty |
| 2 | 216 | 0.50 | 0.76 | 27 | empty |
| 3 | 56 | 0.29 | 0.75 | 13 | empty |
Interfaces
14 interfaces between chains.
- C–D · 592 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–B · 589 Ų buried · 13 hydrogen bonds · protein-nucleic
- E–F · 575 Ų buried · 15 hydrogen bonds · protein-nucleic
- G–H · 569 Ų buried · 12 hydrogen bonds · protein-nucleic
- C–E · 470 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 7F3J · Crystal structure of human YBX2 CSD in complex with m5C RNA in space group P1 · the same entry in another collection · chain H against H, TM-score 1.00
- Q9Y2T7 · AlphaFold monomer V2.0 prediction for Y-box-binding protein 2 (Q9Y2T7) · a predicted model of the same protein · chain E against A, TM-score 0.97
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 Q9Y2T7
- Elsewhere: RCSB PDB 7F3J · PDBe 7F3J · UniProt Q9Y2T7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.