Research workbench
Crystal structure of catalytic fragment of E. COLI alars G237A in complex with glysa
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
- 3HY0
- Type
- protein
- Length
- 882 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
- G5A
- Pockets
- 10 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Alanyl-tRNA synthetase (EC 6.1.1.7) | protein | 441 | 47% helix, 20% strand | P00957 |
Ligands and binding sites
- G5A · 5'-O-(glycylsulfamoyl)adenosine · ligand · 2 copies · chains A, B
- HED · 2-hydroxyethyl disulfide · additive · 4 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 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 | 386 | 0.73 | 0.84 | 46 | G5A |
| 2 | 401 | 0.71 | 0.82 | 49 | G5A |
| 3 | 129 | 0.51 | 0.81 | 23 | empty |
| 4 | 120 | 0.48 | 0.79 | 17 | empty |
| 5 | 89 | 0.40 | 0.78 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 781 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 3HY0 · Crystal Structure of catalytic fragment of E. coli AlaRS G237A in complex with GlySA · 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 B 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 3HY0 · PDBe 3HY0 · UniProt P00957
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