Research workbench
Structure of YTM1 bound to the C-terminal domain of ERB1 in P21 21 2 space group
Analyse Structure of YTM1 bound to the C-terminal domain of ERB1 in P21 21 2 space group in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CXB
- Type
- protein
- Length
- 817 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
- NA, CL
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribosome biogenesis protein YTM1 | protein | 465 | 10% helix, 44% strand | G0SFB5 |
| B | Ribosome biogenesis protein ERB1 | protein | 352 | 7% helix, 45% strand | G0SCK6 |
Ligands and binding sites
- NA · Sodium ion · metal · chains A
- CL · Chloride ion · ion · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 871 | 0.85 | 0.87 | 89 | EDO |
| 2 | 736 | 0.80 | 0.84 | 55 | empty |
| 3 | 348 | 0.60 | 0.77 | 40 | empty |
| 4 | 179 | 0.53 | 0.79 | 34 | EDO |
| 5 | 168 | 0.42 | 0.74 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 1280 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 5CXB · Structure of Ytm1 bound to the C-terminal domain of Erb1 in P21 21 2 space group · 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 1.00
- 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 0.93
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 5CXB · PDBe 5CXB · UniProt G0SFB5 · UniProt G0SCK6
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