Research workbench
Structure of desulfitobacterium hafniense pylsc, a pyrrolysyl tRNA synthetase
Analyse Structure of desulfitobacterium hafniense pylsc, a pyrrolysyl tRNA synthetase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DSQ
- Type
- protein
- Length
- 560 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyrrolysyl-tRNA synthetase
- UniProt
- B0S4P3
- Ligands
- NA, CL
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyrrolysyl-tRNA synthetase | protein | 278 | 38% helix, 22% strand | B0S4P3 |
| B | Pyrrolysyl-tRNA synthetase | protein | 282 | 40% helix, 23% strand | B0S4P3 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 239 | 0.83 | 0.96 | 34 | empty |
| 2 | 796 | 0.76 | 0.80 | 52 | empty |
| 3 | 695 | 0.72 | 0.79 | 53 | NA |
| 4 | 127 | 0.47 | 0.79 | 23 | empty |
| 5 | 193 | 0.47 | 0.75 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 2196 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 3DSQ · Structure of Desulfitobacterium hafniense PylSc, a pyrrolysyl tRNA synthetase · 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 B0S4P3
- Elsewhere: RCSB PDB 3DSQ · PDBe 3DSQ · UniProt B0S4P3
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