Research workbench
Crystal structure of the UTP22 and RRP7 complex from saccharomyces cerevisiae
Analyse Crystal structure of the UTP22 and RRP7 complex from saccharomyces cerevisiae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4M5D
- Type
- protein
- Length
- 1,267 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- U3 small nucleolar RNA-associated protein 22; Ribosomal RNA-processing protein 7
- UniProt
- P53254, P25368
- Ligands
- SO4
- Pockets
- 14 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | U3 small nucleolar RNA-associated protein 22 | protein | 1098 | 44% helix, 16% strand | P53254 |
| B | Ribosomal RNA-processing protein 7 | protein | 169 | 36% helix, 19% strand | P25368 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 11 copies · chains A
- PGE · Triethylene glycol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1049 | 0.84 | 0.85 | 89 | empty |
| 2 | 670 | 0.75 | 0.81 | 72 | SO4 |
| 3 | 617 | 0.73 | 0.80 | 62 | empty |
| 4 | 357 | 0.70 | 0.82 | 45 | empty |
| 5 | 85 | 0.61 | 0.88 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 3177 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 4M5D · Crystal structure of the Utp22 and Rrp7 complex from Saccharomyces cerevisiae · the same entry in another collection · chain A against A, TM-score 1.00
- P53254 · AlphaFold monomer V2.0 prediction for U3 small nucleolar RNA- associated protein 22… · a predicted model of the same protein · chain A against A, TM-score 0.97
- P25368 · AlphaFold monomer V2.0 prediction for ribosomal RNA-processing protein 7 (P25368) · a predicted model of the same protein · chain B against A, TM-score 0.92
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 P53254
- Every structure of UniProt P25368
- Elsewhere: RCSB PDB 4M5D · PDBe 4M5D · UniProt P53254 · UniProt P25368
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