MolNFT v1 · #66691 · protein
Crystal structure of catalytic fragment of E. COLI alars G237A in complex with glysa
3HY0 · Alanyl-tRNA synthetase: “Crystal structure of catalytic fragment of E. COLI alars G237A in complex with glysa”. X-ray diffraction, 1 ligand (G5A), 10 pockets (best druggability 0.73). MolNFT v1 #66691 on GenesisL1: 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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