Research workbench
Crystal structure of mpy-RNase J (mutant S247A), an archaeal RNase J from methanolobus psychrophilus R15, complex with RNA
Analyse Crystal structure of mpy-RNase J (mutant S247A), an archaeal RNase J from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WS2
- Type
- protein + RNA
- Length
- 936 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease J; RNA (5'-R(P*AP*AP*AP*AP*A)-3')
- EC
- 3.1.-.-
- UniProt
- K4MAF9
- Ligands
- ZN, SO4
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonuclease J (EC 3.1.-.-) | protein | 463 | 33% helix, 23% strand | K4MAF9 |
| B | Ribonuclease J (EC 3.1.-.-) | protein | 463 | 33% helix, 23% strand | K4MAF9 |
| C, D | RNA (5'-R(P*AP*AP*AP*AP*A)-3') | rna | 5 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, C, B, D
- SO4 · Sulfate ion · ion · 9 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 522 | 0.69 | 0.79 | 57 | empty |
| 2 | 201 | 0.68 | 0.86 | 38 | empty |
| 3 | 183 | 0.66 | 0.86 | 32 | empty |
| 4 | 77 | 0.55 | 0.86 | 28 | empty |
| 5 | 82 | 0.52 | 0.85 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1543 Ų buried · 35 hydrogen bonds · protein-protein
- B–D · 1089 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–C · 1069 Ų buried · 26 hydrogen bonds · protein-nucleic
Compared structures
- 5WS2 · Crystal structure of mpy-RNase J (mutant S247A), an archaeal RNase J from Methanolobus… · the same entry in another collection · chain D against D, 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 K4MAF9
- Elsewhere: RCSB PDB 5WS2 · PDBe 5WS2 · UniProt K4MAF9
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