MolNFT v1 · #155880 · protein + RNA
Crystal structure of mpy-RNase J (mutant S247A), an archaeal RNase J from methanolobus psychrophilus R15, in complex with 6 nt RNA
6LLB: “Crystal structure of mpy-RNase J (mutant S247A), an archaeal RNase J from methanolobus psychrophilus R15, in…”. X-ray diffraction, 2 ligands (ZN, SO4), 7 pockets (best druggability 0.69). MolNFT v1 #155880 on GenesisL1: 3D…
- PDB
- 6LLB
- Type
- protein + RNA
- Length
- 938 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mpy-RNase J; RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')
- EC
- 3.1.-.-
- Ligands
- ZN, SO4
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mpy-RNase J (EC 3.1.-.-) | protein | 463 | 34% helix, 22% strand | — |
| B | Mpy-RNase J (EC 3.1.-.-) | protein | 463 | 34% helix, 22% strand | — |
| C, D | RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3') | rna | 6 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, C, B, D
- SO4 · Sulfate ion · ion · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 544 | 0.69 | 0.79 | 60 | empty |
| 2 | 232 | 0.68 | 0.85 | 39 | empty |
| 3 | 208 | 0.65 | 0.84 | 32 | empty |
| 4 | 98 | 0.52 | 0.83 | 29 | empty |
| 5 | 79 | 0.47 | 0.82 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1502 Ų buried · 32 hydrogen bonds · protein-protein
- B–D · 1277 Ų buried · 24 hydrogen bonds · protein-nucleic
- A–C · 1273 Ų buried · 24 hydrogen bonds · protein-nucleic
Compared structures
- 6LLB · Crystal structure of mpy-RNase J (mutant S247A), an archaeal RNase J from Methanolobus… · 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
- Elsewhere: RCSB PDB 6LLB · PDBe 6LLB
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