Research workbench
Structure of YTM1 bound to the C-terminal domain of ERB1-R486E
Analyse Structure of YTM1 bound to the C-terminal domain of ERB1-R486E in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CYK
- Type
- protein
- Length
- 804 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosome biogenesis protein YTM1; Ribosome biogenesis protein ERB1
- UniProt
- G0SFB5, G0SCK6
- Ligands
- CL
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribosome biogenesis protein YTM1 | protein | 454 | 7% helix, 41% strand | G0SFB5 |
| B | Ribosome biogenesis protein ERB1 | protein | 350 | 6% helix, 46% strand | G0SCK6 |
Ligands and binding sites
- CL · Chloride ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 933 | 0.84 | 0.85 | 92 | empty |
| 2 | 601 | 0.79 | 0.85 | 56 | empty |
| 3 | 150 | 0.51 | 0.79 | 26 | empty |
| 4 | 165 | 0.49 | 0.77 | 36 | empty |
| 5 | 174 | 0.44 | 0.74 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 1224 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 5CYK · Structure of Ytm1 bound to the C-terminal domain of Erb1-R486E · the same entry in another collection · chain A against A, TM-score 1.00
- G0SCK6 · AlphaFold monomer V2.0 prediction for ribosome biogenesis protein ERB1 (G0SCK6) · a predicted model of the same protein · chain B against A, TM-score 0.99
- G0SFB5 · AlphaFold monomer V2.0 prediction for ribosome biogenesis protein YTM1 (G0SFB5) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 G0SFB5
- Every structure of UniProt G0SCK6
- Elsewhere: RCSB PDB 5CYK · PDBe 5CYK · UniProt G0SFB5 · UniProt G0SCK6
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