Research workbench
Crystal structure of methanosarcina barkeri seryl-tRNA synthetase complexed with serine
Analyse Crystal structure of methanosarcina barkeri seryl-tRNA synthetase complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2CJB
- Type
- protein
- Length
- 969 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Seryl-tRNA synthetase
- EC
- 6.1.1.11
- UniProt
- Q46AN5
- Ligands
- SER, ZN, CL
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Seryl-tRNA synthetase (EC 6.1.1.11) | protein | 474 | 36% helix, 22% strand | Q46AN5 |
| B | Seryl-tRNA synthetase (EC 6.1.1.11) | protein | 495 | 37% helix, 25% strand | Q46AN5 |
Ligands and binding sites
- SER · Serine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 707 | 0.73 | 0.79 | 68 | SER |
| 2 | 70 | 0.71 | 0.96 | 20 | empty |
| 3 | 451 | 0.70 | 0.81 | 45 | SER |
| 4 | 168 | 0.68 | 0.87 | 24 | empty |
| 5 | 403 | 0.60 | 0.76 | 39 | empty |
Interfaces
1 interface between chains.
- A–B · 5239 Ų buried · 71 hydrogen bonds · protein-protein
Compared structures
- 2CJB · Crystal structure of Methanosarcina barkeri seryl-tRNA synthetase complexed with serine · the same entry in another collection · chain B against B, TM-score 1.00
- Q46AN5 · AlphaFold monomer V2.0 prediction for type-2 serine--tRNA ligase (Q46AN5) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q46AN5
- Elsewhere: RCSB PDB 2CJB · PDBe 2CJB · UniProt Q46AN5
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