MolNFT v1 · #111271 · protein
Crystal structure of peptidyl-tRNA hydrolase from a gram-positive bacterium, staphylococcus aureus at 2.25 ångström resolution
4YLY: “Crystal structure of peptidyl-tRNA hydrolase from a gram-positive bacterium, staphylococcus aureus at 2.25…”. X-ray diffraction, 3 pockets (best druggability 0.52). MolNFT v1 #111271 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4YLY
- Type
- protein
- Length
- 395 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
- Q6YP15
- Pockets
- 3 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidyl-tRNA hydrolase (EC 3.1.1.29) | protein | 198 | 42% helix, 22% strand | Q6YP15 |
| B | Peptidyl-tRNA hydrolase (EC 3.1.1.29) | protein | 197 | 43% helix, 23% strand | Q6YP15 |
Ligands and binding sites
- GOL · Glycerol · additive · 5 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 | 261 | 0.52 | 0.75 | 38 | empty |
| 2 | 142 | 0.46 | 0.77 | 18 | empty |
| 3 | 68 | 0.32 | 0.75 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 320 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4YLY · Crystal structure of peptidyl-tRNA hydrolase from a Gram-positive bacterium… · the same entry in another collection · chain A against A, TM-score 1.00
- Q6YP15 · AlphaFold monomer V2.0 prediction for peptidyl-tRNA hydrolase (Q6YP15) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q6YP15
- Elsewhere: RCSB PDB 4YLY · PDBe 4YLY · UniProt Q6YP15
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