MolNFT v1 · #56800 · protein
Crystal structure of seryl-tRNA synthetase from pyrococcus horikoshii complexed with ATP
2ZR2: “Crystal structure of seryl-tRNA synthetase from pyrococcus horikoshii complexed with ATP”. X-ray diffraction, 2 ligands (AMP, SO4), 10 pockets (best druggability 0.75). MolNFT v1 #56800 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2ZR2
- Type
- protein
- Length
- 894 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
- O58441
- Ligands
- AMP, SO4
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Seryl-tRNA synthetase (EC 6.1.1.11) | protein | 447 | 44% helix, 23% strand | O58441 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 776 | 0.75 | 0.80 | 63 | AMP, SO4 |
| 2 | 742 | 0.74 | 0.79 | 54 | AMP, SO4 |
| 3 | 150 | 0.73 | 0.91 | 28 | empty |
| 4 | 92 | 0.36 | 0.75 | 15 | empty |
| 5 | 59 | 0.35 | 0.78 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2411 Ų buried · 48 hydrogen bonds · protein-protein
Compared structures
- 2ZR2 · Crystal structure of seryl-tRNA synthetase from Pyrococcus horikoshii complexed with ATP · the same entry in another collection · chain A against A, TM-score 1.00
- O58441 · AlphaFold monomer V2.0 prediction for serine--tRNA ligase (O58441) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 O58441
- Elsewhere: RCSB PDB 2ZR2 · PDBe 2ZR2 · UniProt O58441
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