MolNFT v1 · #103126 · protein
Phers in complex with compound 2A
4P72 · Phenylalanine--tRNA ligase beta subunit: “Phers in complex with compound 2A”. X-ray diffraction, 1 ligand (2NL), 20 pockets (best druggability 0.85). MolNFT v1 #103126 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4P72
- Type
- protein
- Length
- 2,061 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phenylalanine--tRNA ligase beta subunit; Phenylalanine--tRNA ligase alpha subunit
- EC
- 6.1.1.20
- UniProt
- Q9I0A4, Q9I0A3
- Ligands
- 2NL
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phenylalanine--tRNA ligase beta subunit (EC 6.1.1.20) | protein | 791 | 27% helix, 30% strand | Q9I0A4 |
| C | Phenylalanine--tRNA ligase alpha subunit (EC 6.1.1.20) | protein | 235 | 32% helix, 29% strand | Q9I0A3 |
| D | Phenylalanine--tRNA ligase alpha subunit (EC 6.1.1.20) | protein | 244 | 32% helix, 28% strand | Q9I0A3 |
Ligands and binding sites
- 2NL · 2-{3-[(4-chloropyridin-2-yl)amino]phenoxy}-N-methylacetamide · ligand · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 763 | 0.85 | 0.88 | 71 | empty |
| 2 | 361 | 0.78 | 0.89 | 38 | empty |
| 3 | 1160 | 0.75 | 0.78 | 97 | 2NL |
| 4 | 197 | 0.73 | 0.89 | 25 | empty |
| 5 | 688 | 0.72 | 0.79 | 72 | 2NL |
Interfaces
6 interfaces between chains.
- B–D · 3577 Ų buried · 61 hydrogen bonds · protein-protein
- A–C · 3513 Ų buried · 55 hydrogen bonds · protein-protein
- A–D · 2032 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 1987 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 1560 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 4P72 · PheRS in complex with compound 2a · the same entry in another collection · chain C against C, TM-score 1.00
- Q9I0A3 · AlphaFold monomer V2.0 prediction for phenylalanine--tRNA ligase alpha subunit (Q9I0A3) · a predicted model of the same protein · chain C against A, TM-score 0.95
- Q9I0A4 · AlphaFold monomer V2.0 prediction for phenylalanine--tRNA ligase beta subunit (Q9I0A4) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 Q9I0A4
- Every structure of UniProt Q9I0A3
- Elsewhere: RCSB PDB 4P72 · PDBe 4P72 · UniProt Q9I0A4 · UniProt Q9I0A3
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