MolNFT v1 · #8573 · protein
Prolyl-tRNA synthetase from thermus thermophilus complexed with L-proline
1H4T: “Prolyl-tRNA synthetase from thermus thermophilus complexed with L-proline”. X-ray diffraction, 2 ligands (PRO, ZN), 20 pockets (best druggability 0.83). MolNFT v1 #8573 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1H4T
- Type
- protein
- Length
- 1,856 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prolyl-tRNA synthetase
- EC
- 6.1.1.15
- Ligands
- PRO, ZN
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Prolyl-tRNA synthetase (EC 6.1.1.15) | protein | 464 | 37% helix, 28% strand | — |
Ligands and binding sites
- PRO · Proline · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1134 | 0.83 | 0.84 | 111 | empty |
| 2 | 958 | 0.82 | 0.84 | 89 | empty |
| 3 | 815 | 0.78 | 0.81 | 65 | empty |
| 4 | 574 | 0.70 | 0.79 | 43 | empty |
| 5 | 439 | 0.66 | 0.79 | 44 | PRO |
Interfaces
3 interfaces between chains.
- A–B · 2464 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 2400 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 832 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 1H4T · Prolyl-tRNA synthetase from Thermus thermophilus complexed with L-proline · 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
- Elsewhere: RCSB PDB 1H4T · PDBe 1H4T
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