Research workbench
Crystal structure of human YBX2 csd in complex with M5C RNA in space group P212121
Analyse Crystal structure of human YBX2 csd in complex with M5C RNA in space group… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7F3I
- Type
- protein + RNA
- Length
- 285 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Y-box-binding protein 2; RNA (5'-R(*GP*UP*(5MC)P*CP*(5MC))-3')
- UniProt
- Q9Y2T7
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Y-box-binding protein 2 | protein | 93 | 6% helix, 46% strand | Q9Y2T7 |
| B, D | RNA (5'-R(*GP*UP*(5MC)P*CP*(5MC))-3') | rna | 5 | — | — |
| C, E | Y-box-binding protein 2 | protein | 91 | 7% helix, 49% 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 | 681 | 0.67 | 0.76 | 61 | empty |
| 2 | 69 | 0.37 | 0.78 | 18 | empty |
| 3 | 50 | 0.28 | 0.75 | 13 | empty |
Interfaces
7 interfaces between chains.
- C–D · 757 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–B · 726 Ų buried · 15 hydrogen bonds · protein-nucleic
- C–E · 380 Ų buried · 3 hydrogen bonds · protein-protein
- A–E · 325 Ų buried · 1 hydrogen bond · protein-protein
- D–E · 251 Ų buried · 10 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 7F3I · Crystal structure of human YBX2 CSD in complex with m5C RNA in space group P212121 · the same entry in another collection · chain B against B, 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 C against A, TM-score 0.98
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 7F3I · PDBe 7F3I · UniProt Q9Y2T7
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