Research workbench
Crystal structure of catalytic fragment of E. COLI alars G237A in complex with sersa
Analyse Crystal structure of catalytic fragment of E. COLI alars G237A in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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