MolNFT v1 · #117860 · protein
Crystal structure of mutant-K146A of peptidyl-tRNA hydrolase from vibrio cholerae at 1.63A resolution.
5EKT: “Crystal structure of mutant-K146A of peptidyl-tRNA hydrolase from vibrio cholerae at 1.63A resolution.”. X-ray diffraction, 5 pockets (best druggability 0.47). MolNFT v1 #117860 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5EKT
- Type
- protein
- Length
- 394 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
- Q9KQ21
- Pockets
- 5 · best druggability 0.47
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Peptidyl-tRNA hydrolase (EC 3.1.1.29) | protein | 197 | 43% helix, 22% strand | Q9KQ21 |
Ligands and binding sites
- FLC · Citrate anion · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 119 | 0.47 | 0.79 | 30 | empty |
| 2 | 81 | 0.39 | 0.77 | 15 | empty |
| 3 | 132 | 0.39 | 0.74 | 23 | empty |
| 4 | 71 | 0.33 | 0.75 | 20 | empty |
| 5 | 91 | 0.33 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 985 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 5EKT · Crystal structure of mutant-K146A of peptidyl-tRNA hydrolase from Vibrio cholerae at… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9KQ21 · AlphaFold monomer V2.0 prediction for peptidyl-tRNA hydrolase (Q9KQ21) · 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 Q9KQ21
- Elsewhere: RCSB PDB 5EKT · PDBe 5EKT · UniProt Q9KQ21
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