Research workbench
Crystal structure of catalytic fragment of E. COLI alars in complex with amppcp, ala-AMP and pcp
Analyse Crystal structure of catalytic fragment of E. COLI alars 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
- 3HXY
- 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
- 5AL, MDN, ACP, MG
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alanyl-tRNA synthetase (EC 6.1.1.7) | protein | 441 | 45% helix, 19% strand | P00957 |
Ligands and binding sites
- 5AL · 5'-O-[(R)-{[(2S)-2-aminopropanoyl]oxy}(hydroxy)phosphoryl]adenosine · ligand · chains A
- MDN · Methylenediphosphonic acid · ligand · chains A
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains A
- MG · Magnesium ion · metal · 4 copies · chains A
- HED · 2-hydroxyethyl disulfide · 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 | 398 | 0.72 | 0.83 | 50 | 5AL, MDN, ACP, MG |
| 2 | 84 | 0.40 | 0.78 | 18 | empty |
| 3 | 69 | 0.35 | 0.77 | 13 | empty |
| 4 | 53 | 0.33 | 0.78 | 13 | empty |
| 5 | 54 | 0.28 | 0.75 | 14 | empty |
Compared structures
- 3HXY · Crystal Structure of catalytic fragment of E. coli AlaRS in complex with AMPPCP, Ala-AMP… · 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 3HXY · PDBe 3HXY · UniProt P00957
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