Research workbench
Crystal structure of peptidyl-tRNA hydrolase from vibrio cholerae in space group C2221 at resolution 1.75A.
Analyse Crystal structure of peptidyl-tRNA hydrolase from vibrio cholerae in space… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GVZ
- Type
- protein
- Length
- 194 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidyl-tRNA hydrolase
- EC
- 3.1.1.29
- UniProt
- A5F686
- Ligands
- SO4
- Pockets
- 1 · best druggability 0.35
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidyl-tRNA hydrolase (EC 3.1.1.29) | protein | 194 | 43% helix, 21% strand | A5F686 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 75 | 0.35 | 0.76 | 23 | empty |
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 5GVZ · Crystal structure of Peptidyl-tRNA hydrolase from Vibrio cholerae in space group C2221 at… · the same entry in another collection · chain A against A, TM-score 1.00
- A5F686 · AlphaFold monomer V2.0 prediction for peptidyl-tRNA hydrolase (A5F686) · 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 A5F686
- Elsewhere: RCSB PDB 5GVZ · PDBe 5GVZ · UniProt A5F686
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.