Research workbench
Crystal structure of peptidyl-tRNA hydrolase mutant-N14D from vibrio cholerae
Analyse Crystal structure of peptidyl-tRNA hydrolase mutant-N14D from vibrio cholerae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IMB
- Type
- protein
- Length
- 389 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 0.40
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidyl-tRNA hydrolase (EC 3.1.1.29) | protein | 194 | 43% helix, 21% strand | Q9KQ21 |
| B | Peptidyl-tRNA hydrolase (EC 3.1.1.29) | protein | 195 | 44% helix, 19% strand | Q9KQ21 |
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 | 86 | 0.40 | 0.77 | 20 | empty |
| 2 | 90 | 0.37 | 0.76 | 22 | empty |
| 3 | 98 | 0.37 | 0.75 | 24 | empty |
| 4 | 56 | 0.34 | 0.78 | 16 | empty |
| 5 | 56 | 0.26 | 0.73 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 991 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 5IMB · Crystal structure of peptidyl-tRNA hydrolase mutant-N14D from Vibrio cholerae · 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 1.00
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 5IMB · PDBe 5IMB · UniProt Q9KQ21
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