MolNFT v1 · #184527 · protein
Human prolyl-tRNA synthetase in complex with L-proline and compound 3B
7OT3 · Bifunctional GLUTAMATE/PROLINE--tRNA ligase: “Human prolyl-tRNA synthetase in complex with L-proline and compound 3B”. X-ray diffraction, 4 ligands (PRO, 0W4, SR), 9 pockets (best druggability 0.74). MolNFT v1 #184527 on GenesisL1…
- PDB
- 7OT3
- Type
- protein
- Length
- 979 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, 0W4, SR, ZN
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 36% 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 | 496 | 36% helix, 27% strand | P07814 |
| B | Bifunctional GLUTAMATE/PROLINE--tRNA ligase (EC 6.1.1.17, 6.1.1.15) | protein | 483 | 36% helix, 28% strand | P07814 |
Ligands and binding sites
- PRO · Proline · ligand · 2 copies · chains A, B
- 0W4 · ~{N}-[(2-chlorophenyl)methyl]-3-[(2-chlorophenyl) methylamino]pyrazine-2-carboxamide · ligand · 2 copies · chains A, B
- SR · Strontium ion · metal · 4 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
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 559 | 0.74 | 0.82 | 51 | PRO, 0W4 |
| 2 | 785 | 0.73 | 0.78 | 68 | SR |
| 3 | 498 | 0.73 | 0.82 | 48 | PRO, 0W4 |
| 4 | 643 | 0.68 | 0.77 | 51 | empty |
| 5 | 108 | 0.48 | 0.80 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 2301 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 7OT3 · Human Prolyl-tRNA Synthetase in Complex with L-proline and Compound 3b · 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 B 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 7OT3 · PDBe 7OT3 · UniProt P07814
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