Research workbench
Human seryl-tRNA synthetase dimer complexed with one molecule of trnasec
Analyse Human seryl-tRNA synthetase dimer complexed with one molecule of trnasec in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RQF
- Type
- protein + RNA
- Length
- 988 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Selenocysteine tRNA; Serine--tRNA ligase, cytoplasmic
- EC
- 6.1.1.11
- UniProt
- P49591
- Ligands
- ANP, SER
- Pockets
- 14 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Selenocysteine tRNA | rna | 63 | — | — |
| A | Serine--tRNA ligase, cytoplasmic (EC 6.1.1.11) | protein | 451 | 39% helix, 20% strand | P49591 |
| B | Serine--tRNA ligase, cytoplasmic (EC 6.1.1.11) | protein | 474 | 41% helix, 20% strand | P49591 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- SER · Serine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 82 | 0.77 | 0.99 | 18 | empty |
| 2 | 835 | 0.74 | 0.79 | 68 | SER, ANP |
| 3 | 764 | 0.73 | 0.79 | 49 | ANP, SER |
| 4 | 525 | 0.69 | 0.80 | 36 | empty |
| 5 | 57 | 0.68 | 0.97 | 17 | empty |
Interfaces
2 interfaces between chains.
- A–B · 3040 Ų buried · 45 hydrogen bonds · protein-protein
- C–A · 622 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 4RQF · human Seryl-tRNA synthetase dimer complexed with one molecule of tRNAsec · the same entry in another collection · chain C against C, TM-score 1.00
- P49591 · AlphaFold monomer V2.0 prediction for serine--tRNA ligase, cytoplasmic (P49591) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P49591
- Elsewhere: RCSB PDB 4RQF · PDBe 4RQF · UniProt P49591
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