Research workbench
Histidyl-tRNA synthetase complexed with histidyl-adenylate
Analyse Histidyl-tRNA synthetase complexed with histidyl-adenylate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KMM
- Type
- protein
- Length
- 1,499 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
- HAM
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histidyl-tRNA synthetase (EC 6.1.1.21) | protein | 386 | 41% helix, 23% strand | P60906 |
| B | Histidyl-tRNA synthetase (EC 6.1.1.21) | protein | 364 | 39% helix, 24% strand | P60906 |
| C | Histidyl-tRNA synthetase (EC 6.1.1.21) | protein | 387 | 41% helix, 22% strand | P60906 |
| D | Histidyl-tRNA synthetase (EC 6.1.1.21) | protein | 362 | 39% helix, 24% strand | P60906 |
Ligands and binding sites
- HAM · Histidyl-adenosine monophosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 907 | 0.82 | 0.84 | 108 | empty |
| 2 | 950 | 0.80 | 0.82 | 101 | empty |
| 3 | 1156 | 0.77 | 0.79 | 71 | empty |
| 4 | 250 | 0.70 | 0.86 | 38 | HAM |
| 5 | 267 | 0.69 | 0.85 | 40 | HAM |
Interfaces
6 interfaces between chains.
- A–B · 3959 Ų buried · 67 hydrogen bonds · protein-protein
- C–D · 3896 Ų buried · 65 hydrogen bonds · protein-protein
- B–C · 203 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 135 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 30 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 1KMM · PDBe 1KMM · UniProt P60906
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