Research workbench
Crystal structure of catalytic fragment of E. COLI alars in complex with amppcp
Analyse Crystal structure of catalytic fragment of E. COLI alars in complex with amppcp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HXX
- 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
- ACP, MG
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alanyl-tRNA synthetase (EC 6.1.1.7) | protein | 441 | 47% helix, 18% strand | P00957 |
Ligands and binding sites
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains A
- MG · Magnesium ion · metal · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 440 | 0.71 | 0.82 | 52 | ACP, MG |
| 2 | 207 | 0.56 | 0.79 | 37 | empty |
| 3 | 92 | 0.41 | 0.78 | 21 | empty |
| 4 | 62 | 0.33 | 0.77 | 13 | empty |
Compared structures
- 3HXX · Crystal Structure of catalytic fragment of E. coli AlaRS in complex with AMPPCP · 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 3HXX · PDBe 3HXX · UniProt P00957
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