MolNFT v1 · #98392 · protein
Crystal structure of the human seryl-tRNA synthetase in complex with ser-sa at 2.9 ångström resolution
4L87 · Serine--tRNA ligase, cytoplasmic: “Crystal structure of the human seryl-tRNA synthetase in complex with ser-sa at 2.9 ångström resolution”. X-ray diffraction, 3 ligands (SSA, MG, PO4), 4 pockets (best druggability 0.75). MolNFT v1…
- PDB
- 4L87
- Type
- protein
- Length
- 476 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine--tRNA ligase, cytoplasmic
- EC
- 6.1.1.11
- UniProt
- P49591
- Ligands
- SSA, MG, PO4
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine--tRNA ligase, cytoplasmic (EC 6.1.1.11) | protein | 476 | 39% helix, 20% strand | P49591 |
Ligands and binding sites
- SSA · 5'-O-(N-(L-seryl)-sulfamoyl)adenosine · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- PO4 · Phosphate ion · ion · 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 | 628 | 0.75 | 0.81 | 62 | SSA, PO4, MG |
| 2 | 85 | 0.35 | 0.75 | 21 | empty |
| 3 | 104 | 0.34 | 0.72 | 16 | empty |
| 4 | 87 | 0.32 | 0.73 | 19 | empty |
Compared structures
- 4L87 · Crystal structure of the human seryl-tRNA synthetase in complex with Ser-SA at 2.9… · the same entry in another collection · chain A against A, 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 0.99
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 P49591
- Elsewhere: RCSB PDB 4L87 · PDBe 4L87 · UniProt P49591
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