Research workbench
Human prolyl-tRNA synthetase in complex with L-proline and compound 3C
Analyse Human prolyl-tRNA synthetase in complex with L-proline and compound 3C in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OT1
- Type
- protein
- Length
- 966 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional GLUTAMATE/PROLINE--tRNA ligase
- EC
- 6.1.1.17, 6.1.1.15
- UniProt
- P07814
- Ligands
- PRO, 1AI, SR, ZN
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional GLUTAMATE/PROLINE--tRNA ligase (EC 6.1.1.17, 6.1.1.15) | protein | 481 | 36% helix, 29% strand | P07814 |
| B | Bifunctional GLUTAMATE/PROLINE--tRNA ligase (EC 6.1.1.17, 6.1.1.15) | protein | 485 | 34% helix, 28% strand | P07814 |
Ligands and binding sites
- PRO · Proline · ligand · 2 copies · chains A, B
- 1AI · ~{N}-[(2-methylphenyl)methyl]-3-[(2-methylphenyl) methylamino]pyrazine-2-carboxamide · ligand · 2 copies · chains A, B
- SR · Strontium ion · metal · 6 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 597 | 0.74 | 0.82 | 47 | PRO, 1AI |
| 2 | 540 | 0.74 | 0.82 | 52 | PRO, 1AI |
| 3 | 740 | 0.74 | 0.79 | 70 | empty |
| 4 | 603 | 0.65 | 0.75 | 45 | SR |
| 5 | 119 | 0.48 | 0.79 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 2380 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 7OT1 · Human Prolyl-tRNA Synthetase in Complex with L-proline and Compound 3c · 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 7OT1 · PDBe 7OT1 · UniProt P07814
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