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Crystal structure of archaeoglobus fulgidus alanyl-tRNA synthetase C-terminal dimerization domain
Analyse Crystal structure of archaeoglobus fulgidus alanyl-tRNA synthetase C-terminal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZVF
- Type
- protein
- Length
- 1,355 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alanyl-tRNA synthetase
- EC
- 6.1.1.7
- UniProt
- O28029
- Ligands
- SO4
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 55% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, G | Alanyl-tRNA synthetase (EC 6.1.1.7) | protein | 170 | 55% helix, 19% strand | O28029 |
| C | Alanyl-tRNA synthetase (EC 6.1.1.7) | protein | 166 | 56% helix, 19% strand | O28029 |
| D, E | Alanyl-tRNA synthetase (EC 6.1.1.7) | protein | 170 | 59% helix, 20% strand | O28029 |
| F | Alanyl-tRNA synthetase (EC 6.1.1.7) | protein | 168 | 52% helix, 17% strand | O28029 |
| H | Alanyl-tRNA synthetase (EC 6.1.1.7) | protein | 171 | 54% helix, 21% strand | O28029 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 964 | 0.83 | 0.85 | 91 | empty |
| 2 | 720 | 0.69 | 0.76 | 56 | empty |
| 3 | 177 | 0.63 | 0.84 | 21 | empty |
| 4 | 119 | 0.59 | 0.85 | 17 | empty |
| 5 | 81 | 0.52 | 0.84 | 15 | empty |
Interfaces
16 interfaces between chains.
- A–B · 1625 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 1559 Ų buried · 8 hydrogen bonds · protein-protein
- G–H · 1526 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 1515 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 689 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 52 modified (engineered).
Compared structures
- 2ZVF · Crystal structure of Archaeoglobus fulgidus alanyl-tRNA synthetase C-terminal… · the same entry in another collection · chain H against H, TM-score 1.00
- O28029 · AlphaFold monomer V2.0 prediction for alanine--tRNA ligase (O28029) · a predicted model of the same protein · chain D against A, TM-score 0.94
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 O28029
- Elsewhere: RCSB PDB 2ZVF · PDBe 2ZVF · UniProt O28029
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