MolNFT v1 · #58988 · protein
Crystal structure analysis of the RNase J/UMP complex
3BK2 · Metal dependent hydrolase: “Crystal structure analysis of the RNase J/UMP complex”. X-ray diffraction, 3 ligands (U5P, ZN, SO4), 4 pockets (best druggability 0.74). MolNFT v1 #58988 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3BK2
- Type
- protein
- Length
- 549 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metal dependent hydrolase
- EC
- 3.-.-.-
- UniProt
- Q72JJ7
- Ligands
- U5P, ZN, SO4
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Metal dependent hydrolase (EC 3.-.-.-) | protein | 549 | 34% helix, 26% strand | Q72JJ7 |
Ligands and binding sites
- U5P · Uridine-5'-monophosphate · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- SO4 · Sulfate ion · ion · chains A
- GOL · Glycerol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 526 | 0.74 | 0.82 | 64 | U5P |
| 2 | 108 | 0.54 | 0.83 | 22 | empty |
| 3 | 111 | 0.41 | 0.77 | 18 | empty |
| 4 | 51 | 0.37 | 0.80 | 13 | empty |
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
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 Q72JJ7
- Elsewhere: RCSB PDB 3BK2 · PDBe 3BK2 · UniProt Q72JJ7
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