Research workbench
One ramp protein binding different RNA substrates
Analyse One ramp protein binding different RNA substrates in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QJL
- Type
- protein + RNA
- Length
- 504 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative uncharacterized protein PH0350; RNA (5'-R(*GP*UP*UP*AP*CP*AP*AP*UP*AP*AP*GP*A)-3'…
- UniProt
- O58088
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative uncharacterized protein PH0350 | protein | 240 | 27% helix, 40% strand | O58088 |
| X, R | RNA (5'-R(*GP*UP*UP*AP*CP*AP*AP*UP*AP*AP*GP*A)-3') | rna | 12 | — | — |
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 573 | 0.79 | 0.85 | 53 | empty |
| 2 | 346 | 0.62 | 0.79 | 27 | empty |
| 3 | 59 | 0.28 | 0.74 | 14 | empty |
Interfaces
6 interfaces between chains.
- X–B · 1083 Ų buried · 32 hydrogen bonds · protein-nucleic
- A–R · 1061 Ų buried · 34 hydrogen bonds · protein-nucleic
- A–X · 954 Ų buried · 21 hydrogen bonds · protein-nucleic
- B–R · 951 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–B · 442 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3QJL · One RAMP protein binding different RNA substrates · the same entry in another collection · chain A against A, TM-score 1.00
- O58088 · AlphaFold monomer V2.0 prediction for putative CRISPR-associated endoribonuclease-like… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 O58088
- Elsewhere: RCSB PDB 3QJL · PDBe 3QJL · UniProt O58088
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