MolNFT v1 · #173815 · protein
Crystal structure of human prolyl-tRNA synthetase in complex with NCP26 and L-proline
7BBU · Bifunctional GLUTAMATE/PROLINE--tRNA ligase: “Crystal structure of human prolyl-tRNA synthetase in complex with NCP26 and L-proline”. X-ray diffraction, 5 ligands (PRO, MU5, ZN), 4 pockets (best druggability 0.72). MolNFT v1 #173815…
- PDB
- 7BBU
- Type
- protein
- Length
- 480 residues
- Chains
- 1
- 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, MU5, ZN, NO3, CL
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 29% 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 | 480 | 35% helix, 29% strand | P07814 |
Ligands and binding sites
- PRO · Proline · ligand · chains A
- MU5 · ~{N}-(2,3-dihydro-1~{H}-inden-2-yl)-3-(piperidin-1-ylcarbonylamino)pyrazine-2-carboxamide · ligand · chains A
- ZN · Zinc ion · metal · chains A
- NO3 · Nitrate ion · ion · chains A
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 10 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 565 | 0.72 | 0.80 | 55 | PRO, MU5 |
| 2 | 81 | 0.43 | 0.79 | 21 | EDO |
| 3 | 58 | 0.42 | 0.81 | 13 | EDO |
| 4 | 50 | 0.25 | 0.73 | 14 | empty |
Compared structures
- 7BBU · Crystal Structure of human Prolyl-tRNA synthetase in complex with NCP26 and L-Proline · 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 0.99
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 7BBU · PDBe 7BBU · UniProt P07814
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.