MolNFT v1 · #103459 · protein
Crystal structure of a human cytosolic histidyl-tRNA synthetase, histidine-bound
4PHC · Histidine--tRNA ligase, cytoplasmic: “Crystal structure of a human cytosolic histidyl-tRNA synthetase, histidine-bound”. X-ray diffraction, 1 ligand (HIS), 18 pockets (best druggability 0.82). MolNFT v1 #103459 on GenesisL1: 3D…
- PDB
- 4PHC
- Type
- protein
- Length
- 1,767 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histidine--tRNA ligase, cytoplasmic
- EC
- 6.1.1.21
- UniProt
- P12081
- Ligands
- HIS
- Pockets
- 18 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histidine--tRNA ligase, cytoplasmic (EC 6.1.1.21) | protein | 444 | 44% helix, 20% strand | P12081 |
| B | Histidine--tRNA ligase, cytoplasmic (EC 6.1.1.21) | protein | 441 | 44% helix, 20% strand | P12081 |
| C | Histidine--tRNA ligase, cytoplasmic (EC 6.1.1.21) | protein | 440 | 44% helix, 20% strand | P12081 |
| D | Histidine--tRNA ligase, cytoplasmic (EC 6.1.1.21) | protein | 442 | 44% helix, 20% strand | P12081 |
Ligands and binding sites
- HIS · Histidine · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 863 | 0.82 | 0.85 | 115 | GOL, HIS |
| 2 | 858 | 0.79 | 0.82 | 67 | empty |
| 3 | 675 | 0.79 | 0.84 | 70 | HIS |
| 4 | 813 | 0.79 | 0.82 | 68 | empty |
| 5 | 620 | 0.72 | 0.80 | 53 | HIS |
Interfaces
5 interfaces between chains.
- C–D · 4178 Ų buried · 53 hydrogen bonds · protein-protein
- A–B · 4136 Ų buried · 54 hydrogen bonds · protein-protein
- A–D · 1190 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 190 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 165 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4PHC · Crystal Structure of a human cytosolic histidyl-tRNA synthetase, histidine-bound · the same entry in another collection · chain D against D, TM-score 1.00
- P12081 · AlphaFold monomer V2.0 prediction for histidine--tRNA ligase, cytoplasmic (P12081) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P12081
- Elsewhere: RCSB PDB 4PHC · PDBe 4PHC · UniProt P12081
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