Research workbench
Structural and dynamic studies provide insights into specificity and allosteric regulation of ribonuclease as, a key enzyme in mycobacterial virulence
Analyse Structural and dynamic studies provide insights into specificity and allosteric… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6S0M
- Type
- protein + RNA
- Length
- 319 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3'-5' exoribonuclease; RNA (5'-R(P*G)-3')
- EC
- 3.1.13.-
- UniProt
- A0A045JQ63
- Ligands
- MG
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3'-5' exoribonuclease (EC 3.1.13.-) | protein | 160 | 38% helix, 21% strand | A0A045JQ63 |
| B | 3'-5' exoribonuclease (EC 3.1.13.-) | protein | 158 | 35% helix, 22% strand | A0A045JQ63 |
| C | RNA (5'-R(P*G)-3') | rna | 1 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 299 | 0.57 | 0.76 | 34 | MG |
| 2 | 225 | 0.54 | 0.77 | 31 | MG |
| 3 | 102 | 0.42 | 0.78 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1283 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 239 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–C · 62 Ų buried · 0 hydrogen bonds · protein-nucleic
Compared structures
- 6S0M · Structural and dynamic studies provide insights into specificity and allosteric… · 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 A0A045JQ63
- Elsewhere: RCSB PDB 6S0M · PDBe 6S0M · UniProt A0A045JQ63
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