MolNFT v1 · #110443 · protein + RNA
Crystal structure of RNase J complexed with RNA
4XWW · DR2417: “Crystal structure of RNase J complexed with RNA”. X-ray diffraction, 2 ligands (ZN, MN), 14 pockets (best druggability 0.80). MolNFT v1 #110443 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4XWW
- Type
- protein + RNA
- Length
- 1,100 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DR2417; RNA (5'-D(UP*UP*UP*UP*UP*UP*U)-3')
- UniProt
- H9CZL7
- Ligands
- ZN, MN
- Pockets
- 14 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DR2417 | protein | 545 | 34% helix, 25% strand | H9CZL7 |
| B | DR2417 | protein | 543 | 34% helix, 24% strand | H9CZL7 |
| D, E | RNA (5'-D(UP*UP*UP*UP*UP*UP*U)-3') | rna | 6 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, D, B, E
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1014 | 0.80 | 0.81 | 99 | GOL |
| 2 | 405 | 0.67 | 0.80 | 50 | empty |
| 3 | 135 | 0.52 | 0.80 | 22 | empty |
| 4 | 122 | 0.50 | 0.80 | 18 | empty |
| 5 | 84 | 0.42 | 0.79 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2400 Ų buried · 34 hydrogen bonds · protein-protein
- B–E · 1091 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–D · 1080 Ų buried · 17 hydrogen bonds · protein-nucleic
Compared structures
- 4XWW · Crystal structure of RNase J complexed with RNA · 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 H9CZL7
- Elsewhere: RCSB PDB 4XWW · PDBe 4XWW · UniProt H9CZL7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.