MolNFT v1 · #89240 · protein
Crystal structure of the complex of peptidyl-tRNA hydrolase from pseudomonas aeruginosa with pimelic acid at 2.9 ångström resolution
4DJJ: “Crystal structure of the complex of peptidyl-tRNA hydrolase from pseudomonas aeruginosa with pimelic acid at…”. X-ray diffraction, 1 ligand (PML), 3 pockets (best druggability 0.81). MolNFT v1 #89240 on GenesisL1: 3D structure…
- PDB
- 4DJJ
- Type
- protein
- Length
- 388 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidyl-tRNA hydrolase
- EC
- 3.1.1.29
- UniProt
- Q9HVC3
- Ligands
- PML
- Pockets
- 3 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Peptidyl-tRNA hydrolase (EC 3.1.1.29) | protein | 194 | 42% helix, 21% strand | Q9HVC3 |
Ligands and binding sites
- PML · Pimelic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 891 | 0.81 | 0.84 | 87 | empty |
| 2 | 122 | 0.44 | 0.77 | 26 | PML |
| 3 | 110 | 0.42 | 0.77 | 23 | PML |
Interfaces
1 interface between chains.
- A–B · 598 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 4DJJ · Crystal structure of the complex of Peptidyl-tRNA hydrolase from Pseudomonas aeruginosa… · the same entry in another collection · chain B against B, TM-score 1.00
- Q9HVC3 · AlphaFold monomer V2.0 prediction for peptidyl-tRNA hydrolase (Q9HVC3) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9HVC3
- Elsewhere: RCSB PDB 4DJJ · PDBe 4DJJ · UniProt Q9HVC3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.