Research workbench
Crystal structure of S. aureus seryl-tRNA synthetase complexed to seryl sulfamoyl adenosine
Analyse Crystal structure of S. aureus seryl-tRNA synthetase complexed to seryl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6R1N
- Type
- protein
- Length
- 420 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine--tRNA ligase
- EC
- 6.1.1.11
- UniProt
- X5DWM7
- Ligands
- SSA, MG
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine--tRNA ligase (EC 6.1.1.11) | protein | 420 | 43% helix, 20% strand | X5DWM7 |
Ligands and binding sites
- SSA · 5'-O-(N-(L-seryl)-sulfamoyl)adenosine · ligand · chains A
- MG · Magnesium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
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 | 557 | 0.71 | 0.80 | 47 | SSA, EDO, PEG, MG |
| 2 | 57 | 0.42 | 0.82 | 12 | empty |
| 3 | 82 | 0.34 | 0.75 | 18 | empty |
| 4 | 51 | 0.27 | 0.74 | 13 | EDO |
Compared structures
- 6R1N · Crystal structure of S. aureus seryl-tRNA synthetase complexed to seryl sulfamoyl… · 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 X5DWM7
- Elsewhere: RCSB PDB 6R1N · PDBe 6R1N · UniProt X5DWM7
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