MolNFT v1 · #66686 · protein
Crystal structure of catalytic fragment of E. COLI alars in complex with glysa
3HXV · Alanyl-tRNA synthetase: “Crystal structure of catalytic fragment of E. COLI alars in complex with glysa”. X-ray diffraction, 1 ligand (G5A), 5 pockets (best druggability 0.72). MolNFT v1 #66686 on GenesisL1: 3D structure, binding…
- PDB
- 3HXV
- Type
- protein
- Length
- 441 residues
- Chains
- 1
- 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
- 5 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 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 · chains A
- HED · 2-hydroxyethyl disulfide · additive · 3 copies · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
- BME · Beta-mercaptoethanol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 422 | 0.72 | 0.83 | 52 | G5A |
| 2 | 80 | 0.40 | 0.79 | 21 | empty |
| 3 | 62 | 0.36 | 0.78 | 13 | empty |
| 4 | 51 | 0.31 | 0.77 | 14 | empty |
| 5 | 73 | 0.31 | 0.74 | 17 | empty |
Compared structures
- 3HXV · Crystal Structure of catalytic fragment of E. coli AlaRS 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 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 3HXV · PDBe 3HXV · UniProt P00957
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