MolNFT v1 · #103019 · protein
Structural basis for full-spectrum inhibition of threonyl-tRNA synthetase by borrelidin 1
4P3N · Threonine--tRNA ligase, cytoplasmic: “Structural basis for full-spectrum inhibition of threonyl-tRNA synthetase by borrelidin 1”. X-ray diffraction, 2 ligands (2CR, ZN), 14 pockets (best druggability 0.84). MolNFT v1 #103019 on…
- PDB
- 4P3N
- Type
- protein
- Length
- 1,608 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Threonine--tRNA ligase, cytoplasmic
- EC
- 6.1.1.3
- UniProt
- P26639
- Ligands
- 2CR, ZN
- Pockets
- 14 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Threonine--tRNA ligase, cytoplasmic (EC 6.1.1.3) | protein | 402 | 40% helix, 26% strand | P26639 |
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 · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 977 | 0.84 | 0.86 | 91 | empty |
| 2 | 1097 | 0.84 | 0.85 | 101 | empty |
| 3 | 463 | 0.67 | 0.79 | 45 | 2CR, ZN |
| 4 | 474 | 0.67 | 0.78 | 39 | 2CR, ZN |
| 5 | 546 | 0.66 | 0.77 | 43 | 2CR, ZN |
Interfaces
4 interfaces between chains.
- A–B · 2402 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 2354 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 181 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 169 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4P3N · Structural Basis for Full-Spectrum Inhibition of Threonyl-tRNA Synthetase by Borrelidin 1 · the same entry in another collection · chain A against A, TM-score 1.00
- P26639 · AlphaFold monomer V2.0 prediction for threonine--tRNA ligase 1, cytoplasmic (P26639) · 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 P26639
- Elsewhere: RCSB PDB 4P3N · PDBe 4P3N · UniProt P26639
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