Research workbench
Crystal structure of human prolyl-tRNA synthetase (substrate bound form)
Analyse Crystal structure of human prolyl-tRNA synthetase (substrate bound form) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4K87
- Type
- protein
- Length
- 490 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proline--tRNA ligase
- EC
- 6.1.1.15
- UniProt
- P07814
- Ligands
- ADN, PRO, ZN
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proline--tRNA ligase (EC 6.1.1.15) | protein | 490 | 37% helix, 28% strand | P07814 |
Ligands and binding sites
- ADN · Adenosine · ligand · chains A
- PRO · Proline · ligand · chains A
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 475 | 0.74 | 0.83 | 44 | ADN, PRO |
| 2 | 127 | 0.44 | 0.77 | 26 | empty |
| 3 | 52 | 0.39 | 0.81 | 14 | empty |
| 4 | 92 | 0.38 | 0.76 | 18 | empty |
| 5 | 69 | 0.30 | 0.74 | 13 | empty |
Compared structures
- 4K87 · Crystal structure of human prolyl-tRNA synthetase (substrate bound form) · the same entry in another collection · chain A against A, TM-score 1.00
- P07814 · AlphaFold monomer V2.0 prediction for bifunctional GLUTAMATE/PROLINE --tRNA ligase… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P07814
- Elsewhere: RCSB PDB 4K87 · PDBe 4K87 · UniProt P07814
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