MolNFT v1 · #66692 · protein
Crystal structure of catalytic fragment of E. COLI alars G237A in complex with sersa
3HY1 · Alanyl-tRNA synthetase: “Crystal structure of catalytic fragment of E. COLI alars G237A in complex with sersa”. X-ray diffraction, 3 ligands (SSA, MG, SO4), 8 pockets (best druggability 0.72). MolNFT v1 #66692 on GenesisL1: 3D…
- PDB
- 3HY1
- Type
- protein
- Length
- 860 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alanyl-tRNA synthetase
- EC
- 6.1.1.7
- UniProt
- P00957
- Ligands
- SSA, MG, SO4
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alanyl-tRNA synthetase (EC 6.1.1.7) | protein | 440 | 45% helix, 19% strand | P00957 |
| B | Alanyl-tRNA synthetase (EC 6.1.1.7) | protein | 420 | 48% helix, 19% strand | P00957 |
Ligands and binding sites
- SSA · 5'-O-(N-(L-seryl)-sulfamoyl)adenosine · ligand · chains A
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · chains A
- HED · 2-hydroxyethyl disulfide · additive · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 470 | 0.72 | 0.82 | 55 | SSA, SO4, MG |
| 2 | 527 | 0.68 | 0.79 | 40 | empty |
| 3 | 592 | 0.68 | 0.78 | 56 | empty |
| 4 | 328 | 0.62 | 0.79 | 33 | empty |
| 5 | 339 | 0.62 | 0.78 | 36 | empty |
Interfaces
1 interface between chains.
- A–B · 800 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 3HY1 · Crystal Structure of catalytic fragment of E. coli AlaRS G237A in complex with SerSA · the same entry in another collection · chain A against A, TM-score 1.00
- P00957 · AlphaFold monomer V2.0 prediction for alanine--tRNA ligase (P00957) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P00957
- Elsewhere: RCSB PDB 3HY1 · PDBe 3HY1 · UniProt P00957
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