Research workbench
Crystal structure of catalytic fragment of human alars in complex with aze-sa
Analyse Crystal structure of catalytic fragment of human alars in complex with aze-sa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5V59
- Type
- protein
- Length
- 379 residues
- Chains
- 1
- 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
- 8X1
- Pockets
- 2 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alanine--tRNA ligase, cytoplasmic (EC 6.1.1.7) | protein | 379 | 45% helix, 20% strand | P49588 |
Ligands and binding sites
- 8X1 · 5'-O-{[(2S)-azetidine-2-carbonyl]sulfamoyl}adenosine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 442 | 0.67 | 0.80 | 63 | 8X1 |
| 2 | 75 | 0.34 | 0.75 | 13 | empty |
Compared structures
- 5V59 · Crystal structure of catalytic fragment of human AlaRS in complex with Aze-SA · 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 A 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 5V59 · PDBe 5V59 · UniProt P49588
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