Research workbench
Crystal structure of peptidyl-tRNA hydrolase from pseudomonas aeruginosa with adipic acid at 2.4 ångström resolution
Analyse Crystal structure of peptidyl-tRNA hydrolase from pseudomonas aeruginosa with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DHW
- 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
- 0L1
- Pockets
- 3 · best druggability 0.80
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
- 0L1 · hexanedioic 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 | 773 | 0.80 | 0.84 | 82 | empty |
| 2 | 123 | 0.44 | 0.77 | 25 | 0L1 |
| 3 | 93 | 0.41 | 0.78 | 23 | 0L1 |
Interfaces
1 interface between chains.
- A–B · 605 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 4DHW · Crystal structure of Peptidyl-tRNA hydrolase from Pseudomonas aeruginosa with Adipic acid… · the same entry in another collection · chain A against A, 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 4DHW · PDBe 4DHW · UniProt Q9HVC3
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