Research workbench
Structure of ribosome maturation protein rimm and ribosomal protein S19
Analyse Structure of ribosome maturation protein rimm and ribosomal protein S19 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3A1P
- Type
- protein
- Length
- 492 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosome maturation factor rimm; 30S ribosomal protein S19
- UniProt
- Q5SJH5, Q5SHP2
- Ligands
- UNX
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Ribosome maturation factor rimm | protein | 161 | 11% helix, 48% strand | Q5SJH5 |
| B, D | 30S ribosomal protein S19 | protein | 85 | 31% helix, 19% strand | Q5SHP2 |
Ligands and binding sites
- UNX · Unknown atom or ion · ion · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 855 | 0.78 | 0.81 | 75 | UNX |
| 2 | 250 | 0.58 | 0.79 | 34 | empty |
| 3 | 85 | 0.41 | 0.78 | 12 | empty |
| 4 | 122 | 0.38 | 0.74 | 21 | empty |
| 5 | 74 | 0.35 | 0.76 | 15 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1792 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1672 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 689 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 147 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 98 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3A1P · Structure of Ribosome maturation protein RimM and Ribosomal protein S19 · the same entry in another collection · chain A against A, TM-score 1.00
- Q5SJH5 · AlphaFold monomer V2.0 prediction for ribosome maturation factor rimm (Q5SJH5) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 Q5SJH5
- Every structure of UniProt Q5SHP2
- Elsewhere: RCSB PDB 3A1P · PDBe 3A1P · UniProt Q5SJH5 · UniProt Q5SHP2
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