Research workbench
Crystal structure of the ERB1-YTM1 complex
Analyse Crystal structure of the ERB1-YTM1 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EM2
- Type
- protein
- Length
- 1,631 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosome biogenesis protein ERB1; Ribosome biogenesis protein YTM1
- UniProt
- G0SCK6, G0SFB5
- Ligands
- MG
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Ribosome biogenesis protein ERB1 | protein | 357 | 7% helix, 44% strand | G0SCK6 |
| B | Ribosome biogenesis protein YTM1 | protein | 460 | 8% helix, 44% strand | G0SFB5 |
| D | Ribosome biogenesis protein YTM1 | protein | 457 | 9% helix, 43% strand | G0SFB5 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A, C
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 916 | 0.84 | 0.86 | 93 | EDO |
| 2 | 948 | 0.83 | 0.84 | 93 | EDO |
| 3 | 761 | 0.81 | 0.84 | 55 | EDO |
| 4 | 762 | 0.81 | 0.84 | 53 | empty |
| 5 | 138 | 0.64 | 0.86 | 27 | EDO |
Interfaces
3 interfaces between chains.
- A–B · 1257 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1244 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1007 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 5EM2 · Crystal structure of the Erb1-Ytm1 complex · the same entry in another collection · chain D against D, TM-score 1.00
- G0SCK6 · AlphaFold monomer V2.0 prediction for ribosome biogenesis protein ERB1 (G0SCK6) · a predicted model of the same protein · chain A 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 D 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 G0SCK6
- Every structure of UniProt G0SFB5
- Elsewhere: RCSB PDB 5EM2 · PDBe 5EM2 · UniProt G0SCK6 · UniProt G0SFB5
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