MolNFT v1 · #120752 · protein + RNA
Crystal structure of mpy-RNase J (mutant H84A), an archaeal RNase J from methanolobus psychrophilus R15, complex with RNA
5HAB · Ribonuclease J: “Crystal structure of mpy-RNase J (mutant H84A), an archaeal RNase J from methanolobus psychrophilus R15…”. X-ray diffraction, 1 ligand (SO4), 8 pockets (best druggability 0.70). MolNFT v1 #120752 on GenesisL1: 3D…
- PDB
- 5HAB
- Type
- protein + RNA
- Length
- 929 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
- SO4
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonuclease J (EC 3.1.-.-) | protein | 456 | 32% helix, 23% strand | K4MAF9 |
| B | Ribonuclease J (EC 3.1.-.-) | protein | 463 | 32% helix, 23% strand | K4MAF9 |
| C, D | RNA (5'-R(P*AP*AP*AP*AP*A)-3') | rna | 5 | — | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 9 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 244 | 0.70 | 0.86 | 30 | empty |
| 2 | 202 | 0.69 | 0.86 | 24 | empty |
| 3 | 497 | 0.67 | 0.78 | 43 | empty |
| 4 | 99 | 0.54 | 0.84 | 29 | empty |
| 5 | 88 | 0.52 | 0.84 | 29 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1535 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 1124 Ų buried · 22 hydrogen bonds · protein-nucleic
- B–D · 1065 Ų buried · 20 hydrogen bonds · protein-nucleic
Compared structures
- 5HAB · Crystal structure of mpy-RNase J (mutant H84A), 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
- Every structure of UniProt K4MAF9
- Elsewhere: RCSB PDB 5HAB · PDBe 5HAB · UniProt K4MAF9
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