MolNFT v1 · #176518 · protein
Plasmodium falciparum cytoplasmic phenylalanyl-tRNA synthetase in complex with BRD7929
7DPI · Phenylalanine--tRNA ligase: “Plasmodium falciparum cytoplasmic phenylalanyl-tRNA synthetase in complex with BRD7929”. X-ray diffraction, 2 ligands (B79, MG), 20 pockets (best druggability 0.86). MolNFT v1 #176518 on GenesisL1: 3D…
- PDB
- 7DPI
- Type
- protein
- Length
- 1,640 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phenylalanine--tRNA ligase; Phenylalanyl-tRNA synthetase beta subunit
- EC
- 6.1.1.20
- UniProt
- Q8I246, W7JTS1
- Ligands
- B79, MG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phenylalanine--tRNA ligase (EC 6.1.1.20) | protein | 290 | 29% helix, 18% strand | Q8I246 |
| C | Phenylalanine--tRNA ligase (EC 6.1.1.20) | protein | 292 | 27% helix, 17% strand | Q8I246 |
| B | Phenylalanyl-tRNA synthetase beta subunit (EC 6.1.1.20) | protein | 536 | 27% helix, 14% strand | W7JTS1 |
| D | Phenylalanyl-tRNA synthetase beta subunit (EC 6.1.1.20) | protein | 522 | 24% helix, 17% strand | W7JTS1 |
Ligands and binding sites
- B79 · (8R,9S,10S)-10-[(dimethylamino)methyl]-N-(4-methoxyphenyl)-9-[4-(2-phenylethynyl)phenyl]-1,6-diazabicyclo[6.2.0]decane-6-carboxamide · ligand · 2 copies · chains A, C
- MG · Magnesium ion · metal · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 934 | 0.86 | 0.87 | 119 | empty |
| 2 | 1008 | 0.84 | 0.85 | 116 | empty |
| 3 | 910 | 0.84 | 0.86 | 130 | empty |
| 4 | 349 | 0.80 | 0.90 | 49 | empty |
| 5 | 245 | 0.70 | 0.86 | 36 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2270 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1964 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 1609 Ų buried · 10 hydrogen bonds · protein-protein
- C–B · 1390 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 123 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7DPI · Plasmodium falciparum cytoplasmic Phenylalanyl-tRNA synthetase in complex with BRD7929 · 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 Q8I246
- Every structure of UniProt W7JTS1
- Elsewhere: RCSB PDB 7DPI · PDBe 7DPI · UniProt Q8I246 · UniProt W7JTS1
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