MolNFT v1 · #174306 · protein
Crystal structure of peptidyl-tRNA hydrolase from klebsiella pneumoniae
7BRD: “Crystal structure of peptidyl-tRNA hydrolase from klebsiella pneumoniae”. X-ray diffraction, 2 ligands (CL, SO4), 4 pockets (best druggability 0.51). MolNFT v1 #174306 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7BRD
- Type
- protein
- Length
- 387 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
- A0A2V3K250
- Ligands
- CL, SO4
- Pockets
- 4 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidyl-tRNA hydrolase (EC 3.1.1.29) | protein | 193 | 46% helix, 21% strand | A0A2V3K250 |
| B | Peptidyl-tRNA hydrolase (EC 3.1.1.29) | protein | 194 | 42% helix, 21% strand | A0A2V3K250 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- ACT · Acetate ion · additive · 9 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
- PGE · Triethylene glycol · additive · chains A
- BME · Beta-mercaptoethanol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 190 | 0.51 | 0.77 | 27 | ACT |
| 2 | 52 | 0.33 | 0.78 | 18 | CL |
| 3 | 50 | 0.31 | 0.77 | 19 | empty |
| 4 | 62 | 0.29 | 0.74 | 16 | ACT, SO4 |
Interfaces
1 interface between chains.
- A–B · 712 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 7BRD · Crystal structure of Peptidyl-tRNA hydrolase from Klebsiella pneumoniae · the same entry in another collection · 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 A0A2V3K250
- Elsewhere: RCSB PDB 7BRD · PDBe 7BRD · UniProt A0A2V3K250
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.