Research workbench
Human seryl-tRNA synthetase dimer complexed with two molecules of trnasec
Analyse Human seryl-tRNA synthetase dimer complexed with two molecules of trnasec in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RQE
- Type
- protein + RNA
- Length
- 1,079 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine--tRNA ligase, cytoplasmic; Selenocysteine tRNA
- EC
- 6.1.1.11
- UniProt
- P49591
- Ligands
- SER, ANP
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine--tRNA ligase, cytoplasmic (EC 6.1.1.11) | protein | 460 | 40% helix, 19% strand | P49591 |
| C | Serine--tRNA ligase, cytoplasmic (EC 6.1.1.11) | protein | 452 | 40% helix, 19% strand | P49591 |
| B | Selenocysteine tRNA | rna | 84 | — | — |
| D | Selenocysteine tRNA | rna | 83 | — | — |
Ligands and binding sites
- SER · Serine · ligand · 2 copies · chains A, C
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 629 | 0.75 | 0.82 | 69 | SER, ANP |
| 2 | 622 | 0.75 | 0.82 | 61 | SER, ANP |
| 3 | 67 | 0.75 | 0.99 | 18 | empty |
| 4 | 1050 | 0.73 | 0.77 | 71 | empty |
| 5 | 691 | 0.71 | 0.79 | 53 | empty |
Interfaces
4 interfaces between chains.
- A–C · 3002 Ų buried · 46 hydrogen bonds · protein-protein
- A–B · 495 Ų buried · 3 hydrogen bonds · protein-nucleic
- C–D · 465 Ų buried · 4 hydrogen bonds · protein-nucleic
- A–D · 16 Ų buried · 0 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4RQE · human Seryl-tRNA synthetase dimer complexed with two molecules 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 C 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 4RQE · PDBe 4RQE · UniProt P49591
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.