Research workbench
Precursor ribosomal RNA processing complex, state 1.
Analyse Precursor ribosomal RNA processing complex, state 1. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OF3
- Type
- protein
- Length
- 1,430 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease; CLP1_P domain-containing protein
- UniProt
- G0SGE9, G0S263
- Ligands
- AGS, MG
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 2 distinct chains · 35% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Ribonuclease | protein | 187 | 62% helix, 3% strand | G0SGE9 |
| B, E | CLP1_P domain-containing protein | protein | 528 | 25% helix, 25% strand | G0S263 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 2 copies · chains B, E
- MG · Magnesium ion · metal · 2 copies · chains B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1091 | 0.79 | 0.81 | 107 | AGS, MG |
| 2 | 627 | 0.75 | 0.81 | 56 | AGS, MG |
| 3 | 175 | 0.73 | 0.90 | 27 | empty |
| 4 | 166 | 0.72 | 0.90 | 25 | empty |
| 5 | 427 | 0.69 | 0.80 | 61 | empty |
Interfaces
5 interfaces between chains.
- D–E · 2161 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 2159 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 1172 Ų buried · 3 hydrogen bonds · protein-protein
- A–E · 429 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 417 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6OF3 · Precursor ribosomal RNA processing complex, State 1. · the same entry in another collection · chain A against A, TM-score 1.00
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 G0SGE9
- Every structure of UniProt G0S263
- Elsewhere: RCSB PDB 6OF3 · PDBe 6OF3 · UniProt G0SGE9 · UniProt G0S263
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