MolNFT v1 · #21570 · protein
Crystal structures at 2.5 ångströms resolution of seryl-tRNA synthetase complexed with two different analogues of seryl-adenylate
1SES: “Crystal structures at 2.5 ångströms resolution of seryl-tRNA synthetase complexed with two different…”. X-ray diffraction, 2 ligands (AHX, AMP), 7 pockets (best druggability 0.76). MolNFT v1 #21570 on GenesisL1: 3D structure…
- PDB
- 1SES
- Type
- protein
- Length
- 842 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
- P34945
- Ligands
- AHX, AMP
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Seryl-tRNA synthetase (EC 6.1.1.11) | protein | 421 | 44% helix, 22% strand | P34945 |
Ligands and binding sites
- AHX · Seryl-hydroxamate-adenosine monophosphate · ligand · chains A
- AMP · Adenosine monophosphate · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 529 | 0.76 | 0.84 | 54 | AMP |
| 2 | 607 | 0.74 | 0.81 | 61 | AHX |
| 3 | 75 | 0.55 | 0.86 | 18 | empty |
| 4 | 106 | 0.41 | 0.76 | 14 | empty |
| 5 | 90 | 0.39 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2281 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 1SES · Crystal structures at 2.5 ångströms resolution of seryl-tRNA synthetase complexed with… · the same entry in another collection · chain B against B, TM-score 1.00
- P34945 · AlphaFold monomer V2.0 prediction for serine--tRNA ligase (P34945) · 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 P34945
- Elsewhere: RCSB PDB 1SES · PDBe 1SES · UniProt P34945
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