Research workbench
Crystal structure of REA1-MIDAS/YTM1-ubl complex from chaetomium thermophilum
Analyse Crystal structure of REA1-MIDAS/YTM1-ubl complex from chaetomium thermophilum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QTB
- Type
- protein
- Length
- 679 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MIDASIN,MIDASIN; Ribosome biogenesis protein YTM1
- UniProt
- G0SHE6, G0SFB5
- Ligands
- MG
- Pockets
- 9 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MIDASIN,MIDASIN | protein | 254 | 46% helix, 22% strand | G0SHE6 |
| B, E | Ribosome biogenesis protein YTM1 | protein | 87 | 25% helix, 30% strand | G0SFB5 |
| D | MIDASIN,MIDASIN | protein | 251 | 51% helix, 22% strand | G0SHE6 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B, D, E
- GOL · Glycerol · additive · 3 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 195 | 0.69 | 0.87 | 28 | GOL |
| 2 | 167 | 0.67 | 0.87 | 35 | empty |
| 3 | 94 | 0.60 | 0.87 | 21 | GOL |
| 4 | 90 | 0.57 | 0.86 | 22 | GOL |
| 5 | 228 | 0.53 | 0.77 | 35 | empty |
Interfaces
3 interfaces between chains.
- A–D · 1314 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 1144 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1107 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 6QTB · Crystal structure of Rea1-MIDAS/Ytm1-UBL complex from Chaetomium thermophilum · the same entry in another collection · chain A 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 B against A, TM-score 0.99
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 G0SHE6
- Every structure of UniProt G0SFB5
- Elsewhere: RCSB PDB 6QTB · PDBe 6QTB · UniProt G0SHE6 · UniProt G0SFB5
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