Research workbench
Crystal structure of E.COLI histidyl-tRNA synthetase complexed with a histidyl-adenylate analogue
Analyse Crystal structure of E.COLI histidyl-tRNA synthetase complexed with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2EL9
- Type
- protein
- Length
- 1,505 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histidyl-tRNA synthetase
- EC
- 6.1.1.21
- UniProt
- P60906
- Ligands
- HSS
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histidyl-tRNA synthetase (EC 6.1.1.21) | protein | 372 | 36% helix, 20% strand | P60906 |
| B | Histidyl-tRNA synthetase (EC 6.1.1.21) | protein | 376 | 38% helix, 24% strand | P60906 |
| C | Histidyl-tRNA synthetase (EC 6.1.1.21) | protein | 372 | 37% helix, 23% strand | P60906 |
| D | Histidyl-tRNA synthetase (EC 6.1.1.21) | protein | 385 | 38% helix, 24% strand | P60906 |
Ligands and binding sites
- HSS · 5'-O-[(L-histidylamino)sulfonyl]adenosine · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 953 | 0.81 | 0.83 | 126 | empty |
| 2 | 863 | 0.81 | 0.83 | 110 | empty |
| 3 | 321 | 0.69 | 0.83 | 43 | HSS |
| 4 | 319 | 0.68 | 0.83 | 41 | HSS |
| 5 | 248 | 0.67 | 0.84 | 39 | HSS |
Interfaces
4 interfaces between chains.
- C–D · 4084 Ų buried · 72 hydrogen bonds · protein-protein
- A–B · 4040 Ų buried · 74 hydrogen bonds · protein-protein
- B–D · 143 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 133 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2EL9 · Crystal structure of E.coli Histidyl-tRNA synthetase complexed with a histidyl-adenylate… · the same entry in another collection · chain B against B, TM-score 1.00
- P60906 · AlphaFold monomer V2.0 prediction for histidine--tRNA ligase (P60906) · a predicted model of the same protein · chain C against A, TM-score 0.95
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 P60906
- Elsewhere: RCSB PDB 2EL9 · PDBe 2EL9 · UniProt P60906
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