MolNFT v1 · #103021 · protein
Structural basis for full-spectrum inhibition of threonyl-tRNA synthetase by borrelidin 3
4P3P · Threonine--tRNA ligase: “Structural basis for full-spectrum inhibition of threonyl-tRNA synthetase by borrelidin 3”. X-ray diffraction, 2 ligands (2CR, ZN), 9 pockets (best druggability 0.85). MolNFT v1 #103021 on GenesisL1: 3D…
- PDB
- 4P3P
- Type
- protein
- Length
- 802 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Threonine--tRNA ligase
- EC
- 6.1.1.3
- UniProt
- P0A8M3
- Ligands
- 2CR, ZN
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Threonine--tRNA ligase (EC 6.1.1.3) | protein | 401 | 38% helix, 28% strand | P0A8M3 |
Ligands and binding sites
- 2CR · (1R,2R)-2-[(2S,4E,6E,8R,9S,11R,13S,15S,16S)-7-cyano-8, 16-dihydroxy-9,11,13,15-tetramethyl-18-oxooxacyclooctadeca-4,6-dien-2-yl]cyclopentanecarboxylic acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 5 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 280 | 0.85 | 0.96 | 46 | GOL |
| 2 | 449 | 0.70 | 0.81 | 52 | GOL |
| 3 | 419 | 0.68 | 0.80 | 38 | GOL |
| 4 | 427 | 0.66 | 0.79 | 38 | 2CR |
| 5 | 407 | 0.65 | 0.79 | 40 | 2CR |
Interfaces
1 interface between chains.
- A–B · 2168 Ų buried · 43 hydrogen bonds · protein-protein
Compared structures
- 4P3P · Structural Basis for Full-Spectrum Inhibition of Threonyl-tRNA Synthetase by Borrelidin 3 · the same entry in another collection · chain B against B, TM-score 1.00
- P0A8M3 · AlphaFold monomer V2.0 prediction for threonine--tRNA ligase (P0A8M3) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P0A8M3
- Elsewhere: RCSB PDB 4P3P · PDBe 4P3P · UniProt P0A8M3
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