MolNFT v1 · #12626 · protein
Histidyl-tRNA synthetase complexed with histidinol and ATP
1KMN: “Histidyl-tRNA synthetase complexed with histidinol and ATP”. X-ray diffraction, 2 ligands (HSO, ATP), 16 pockets (best druggability 0.81). MolNFT v1 #12626 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1KMN
- Type
- protein
- Length
- 1,494 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
- HSO, ATP
- Pockets
- 16 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histidyl-tRNA synthetase (EC 6.1.1.21) | protein | 379 | 40% helix, 22% strand | P60906 |
| B | Histidyl-tRNA synthetase (EC 6.1.1.21) | protein | 364 | 38% helix, 23% strand | P60906 |
| C | Histidyl-tRNA synthetase (EC 6.1.1.21) | protein | 387 | 40% helix, 22% strand | P60906 |
| D | Histidyl-tRNA synthetase (EC 6.1.1.21) | protein | 364 | 38% helix, 23% strand | P60906 |
Ligands and binding sites
- HSO · L-histidinol · ligand · 4 copies · chains A, B, C, D
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 762 | 0.81 | 0.84 | 103 | empty |
| 2 | 779 | 0.80 | 0.84 | 96 | empty |
| 3 | 807 | 0.77 | 0.81 | 64 | empty |
| 4 | 288 | 0.69 | 0.84 | 41 | HSO, ATP |
| 5 | 225 | 0.68 | 0.86 | 44 | HSO, ATP |
Interfaces
6 interfaces between chains.
- A–B · 3943 Ų buried · 66 hydrogen bonds · protein-protein
- C–D · 3881 Ų buried · 68 hydrogen bonds · protein-protein
- B–C · 239 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 154 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 105 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
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 1KMN · PDBe 1KMN · UniProt P60906
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