Research workbench
Plasmodium vivax cytoplasmic phenylalanyl-tRNA synthetase in complex with BRD1389
Analyse Plasmodium vivax cytoplasmic phenylalanyl-tRNA synthetase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BY6
- Type
- protein
- Length
- 905 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phenylalanyl-tRNA synthetase beta chain, putative
- EC
- 6.1.1.20
- UniProt
- A5K9S0, A5K464
- Ligands
- FB9, MG
- Pockets
- 15 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phenylalanyl-tRNA synthetase beta chain, putative (EC 6.1.1.20) | protein | 299 | 30% helix, 23% strand | A5K9S0 |
| B | Phenylalanyl-tRNA synthetase beta chain, putative (EC 6.1.1.20) | protein | 606 | 29% helix, 24% strand | A5K464 |
Ligands and binding sites
- FB9 · (3S,4R,8R,9R,10S)-N-(4-cyclopropyloxyphenyl)-10-(methoxymethyl)-3,4-bis(oxidanyl)-9-[4-(2-phenylethynyl)phenyl]-1,6-diazabicyclo[6.2.0]decane-6-carboxamide · ligand · chains A
- MG · Magnesium ion · metal · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1186 | 0.82 | 0.83 | 143 | FB9 |
| 2 | 1068 | 0.81 | 0.82 | 109 | empty |
| 3 | 135 | 0.79 | 0.96 | 23 | empty |
| 4 | 57 | 0.62 | 0.92 | 20 | empty |
| 5 | 107 | 0.61 | 0.87 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 2962 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 7BY6 · Plasmodium vivax cytoplasmic Phenylalanyl-tRNA synthetase in complex with BRD1389 · 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
- Every structure of UniProt A5K9S0
- Every structure of UniProt A5K464
- Elsewhere: RCSB PDB 7BY6 · PDBe 7BY6 · UniProt A5K9S0 · UniProt A5K464
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