MolNFT v1 · #117286 · protein
Crystal structure of a histidyl-tRNA synthetase from acinetobacter baumannii with bound L-histidine and ATP
5E3I · Histidine--tRNA ligase: “Crystal structure of a histidyl-tRNA synthetase from acinetobacter baumannii with bound L-histidine and ATP”. X-ray diffraction, 3 ligands (ATP, HIS, MG), 10 pockets (best druggability 0.83). MolNFT v1…
- PDB
- 5E3I
- Type
- protein
- Length
- 786 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histidine--tRNA ligase
- EC
- 6.1.1.21
- UniProt
- A0A086HW61
- Ligands
- ATP, HIS, MG
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histidine--tRNA ligase (EC 6.1.1.21) | protein | 388 | 40% helix, 23% strand | A0A086HW61 |
| B | Histidine--tRNA ligase (EC 6.1.1.21) | protein | 398 | 41% helix, 22% strand | A0A086HW61 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- HIS · Histidine · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 858 | 0.83 | 0.85 | 95 | empty |
| 2 | 268 | 0.71 | 0.86 | 38 | MG, ATP, HIS |
| 3 | 278 | 0.70 | 0.85 | 40 | MG, ATP, HIS |
| 4 | 229 | 0.61 | 0.81 | 36 | empty |
| 5 | 253 | 0.59 | 0.80 | 38 | empty |
Interfaces
1 interface between chains.
- A–B · 4293 Ų buried · 70 hydrogen bonds · protein-protein
Compared structures
- 5E3I · Crystal Structure of a Histidyl-tRNA synthetase from Acinetobacter baumannii with bound… · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A086HW61
- Elsewhere: RCSB PDB 5E3I · PDBe 5E3I · UniProt A0A086HW61
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