MolNFT v1 · #178064 · protein + RNA
Crystal structure of human YBX2 csd in complex with M5C RNA in space group P212121
7F3I · Y-box-binding protein 2: “Crystal structure of human YBX2 csd in complex with M5C RNA in space group P212121”. X-ray diffraction, 3 pockets (best druggability 0.67). MolNFT v1 #178064 on GenesisL1: 3D structure, binding sites and…
- 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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