Research workbench
Crystal structure of archaeoglobus fulgidus O-phosphoseryl- tRNA synthetase complexed with trnacys
Analyse Crystal structure of archaeoglobus fulgidus O-phosphoseryl- tRNA synthetase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DU4
- Type
- protein + RNA
- Length
- 1,002 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA; O-phosphoseryl-tRNA synthetase
- EC
- 6.1.1.-
- UniProt
- O30126
- Pockets
- 13 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | TRNA | rna | 71 | — | — |
| A | O-phosphoseryl-tRNA synthetase (EC 6.1.1.-) | protein | 466 | 32% helix, 27% strand | O30126 |
| B | O-phosphoseryl-tRNA synthetase (EC 6.1.1.-) | protein | 465 | 33% helix, 28% strand | O30126 |
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 85 | 0.77 | 0.98 | 18 | empty |
| 2 | 654 | 0.72 | 0.79 | 54 | empty |
| 3 | 579 | 0.70 | 0.79 | 52 | empty |
| 4 | 732 | 0.67 | 0.76 | 44 | empty |
| 5 | 433 | 0.65 | 0.78 | 37 | empty |
Interfaces
2 interfaces between chains.
- A–B · 3211 Ų buried · 50 hydrogen bonds · protein-protein
- C–A · 718 Ų buried · 27 hydrogen bonds · protein-nucleic
Compared structures
- 2DU4 · Crystal structure of Archaeoglobus fulgidus O-phosphoseryl-tRNA synthetase complexed with… · the same entry in another collection · chain C against C, TM-score 1.00
- O30126 · AlphaFold monomer V2.0 prediction for O-phosphoserine--TRNA(CYS) ligase (O30126) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 O30126
- Elsewhere: RCSB PDB 2DU4 · PDBe 2DU4 · UniProt O30126
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