Research workbench
Structure of thermus thermophilus CSE3 bound to an RNA representing a product mimic complex
Analyse Structure of thermus thermophilus CSE3 bound to an RNA representing a product… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QRP
- Type
- protein + RNA
- Length
- 230 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative uncharacterized protein TTHB192; RNA (5'-R(*GP*UP*CP*CP*CP*CP*AP*CP*(PGP))-3')…
- UniProt
- Q53WG9
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.45
Structure
x-ray diffraction · 3 distinct chains · 26% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative uncharacterized protein TTHB192 | protein | 214 | 26% helix, 40% strand | Q53WG9 |
| B | RNA (5'-R(*GP*UP*CP*CP*CP*CP*AP*CP*(PGP))-3') | rna | 9 | — | — |
| C | RNA (5'-R(P*(U5P)P*GP*UP*GP*GP*GP*G)-3') | rna | 7 | — | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 100 | 0.45 | 0.79 | 20 | empty |
| 2 | 127 | 0.43 | 0.76 | 23 | empty |
| 3 | 125 | 0.40 | 0.75 | 21 | SO4 |
Interfaces
3 interfaces between chains.
- A–C · 733 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–B · 563 Ų buried · 17 hydrogen bonds · protein-nucleic
- B–C · 304 Ų buried · 32 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3QRP · Structure of Thermus Thermophilus Cse3 bound to an RNA representing a product mimic… · the same entry in another collection · chain A against A, TM-score 1.00
- Q53WG9 · AlphaFold monomer V2.0 prediction for CRISPR-associated endoribonuclease CSE3 (Q53WG9) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q53WG9
- Elsewhere: RCSB PDB 3QRP · PDBe 3QRP · UniProt Q53WG9
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