MolNFT v1 · #159121 · protein
Precursor ribosomal RNA processing complex, state 2.
6OF2 · Ribonuclease: “Precursor ribosomal RNA processing complex, state 2.”. Electron microscopy, 2 ligands (AGS, MG), 20 pockets (best druggability 0.78). MolNFT v1 #159121 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6OF2
- Type
- protein
- Length
- 1,422 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 0.78
Structure
electron microscopy · 2 distinct chains · 35% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Ribonuclease | protein | 183 | 64% helix, 3% strand | G0SGE9 |
| B, E | CLP1_P domain-containing protein | protein | 528 | 24% helix, 24% 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 974 | 0.78 | 0.80 | 101 | AGS, MG |
| 2 | 187 | 0.72 | 0.89 | 27 | empty |
| 3 | 592 | 0.72 | 0.80 | 55 | AGS, MG |
| 4 | 114 | 0.70 | 0.91 | 24 | empty |
| 5 | 125 | 0.70 | 0.90 | 24 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2173 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 2160 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 1284 Ų buried · 4 hydrogen bonds · protein-protein
- A–E · 491 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 478 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6OF2 · Precursor ribosomal RNA processing complex, State 2. · 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 6OF2 · PDBe 6OF2 · UniProt G0SGE9 · UniProt G0S263
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