MolNFT v1 · #109843 · protein
Crystal structure of human alars catalytic domain with R329H mutation
4XEO · Alanine--tRNA ligase, cytoplasmic: “Crystal structure of human alars catalytic domain with R329H mutation”. X-ray diffraction, 3 ligands (A5A, MG, SO4), 7 pockets (best druggability 0.76). MolNFT v1 #109843 on GenesisL1: 3D…
- PDB
- 4XEO
- Type
- protein
- Length
- 762 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alanine--tRNA ligase, cytoplasmic
- EC
- 6.1.1.7
- UniProt
- P49588
- Ligands
- A5A, MG, SO4
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alanine--tRNA ligase, cytoplasmic (EC 6.1.1.7) | protein | 384 | 43% helix, 19% strand | P49588 |
| B | Alanine--tRNA ligase, cytoplasmic (EC 6.1.1.7) | protein | 378 | 44% helix, 20% strand | P49588 |
Ligands and binding sites
- A5A · 5'-O-(N-(L-alanyl)-sulfamoyl)adenosine · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 911 | 0.76 | 0.79 | 82 | GOL |
| 2 | 424 | 0.70 | 0.82 | 49 | A5A, MG |
| 3 | 306 | 0.63 | 0.80 | 43 | A5A, MG |
| 4 | 111 | 0.40 | 0.75 | 15 | GOL |
| 5 | 52 | 0.33 | 0.78 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 616 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4XEO · Crystal Structure of human AlaRS catalytic domain with R329H mutation · the same entry in another collection · chain A against A, TM-score 1.00
- P49588 · AlphaFold monomer V2.0 prediction for alanine--tRNA ligase, cytoplasmic (P49588) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P49588
- Elsewhere: RCSB PDB 4XEO · PDBe 4XEO · UniProt P49588
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