MolNFT v1 · #87979 · protein
Structure of pyrrolysyl-tRNA synthetase in complex with adenylated butyryl lysine
4CH3 · Pyrrolysine--tRNA ligase: “Structure of pyrrolysyl-tRNA synthetase in complex with adenylated butyryl lysine”. X-ray diffraction, 2 ligands (YLB, MG), 3 pockets (best druggability 0.66). MolNFT v1 #87979 on GenesisL1: 3D structure…
- PDB
- 4CH3
- Type
- protein
- Length
- 267 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyrrolysine--tRNA ligase
- EC
- 6.1.1.26
- UniProt
- Q8PWY1
- Ligands
- YLB, MG
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyrrolysine--tRNA ligase (EC 6.1.1.26) | protein | 267 | 39% helix, 22% strand | Q8PWY1 |
Ligands and binding sites
- YLB · 5'-O-({[(2R)-2-amino-6-(butanoylamino)hexanoyl]oxy}phosphinato)adenosine · ligand · chains A
- MG · Magnesium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 356 | 0.66 | 0.80 | 40 | YLB |
| 2 | 61 | 0.35 | 0.78 | 25 | EDO |
| 3 | 74 | 0.31 | 0.74 | 16 | empty |
Compared structures
- 4CH3 · Structure of pyrrolysyl-tRNA synthetase in complex with adenylated butyryl lysine · the same entry in another collection · chain A against A, TM-score 1.00
- Q8PWY1 · AlphaFold monomer V2.0 prediction for pyrrolysine--tRNA ligase (Q8PWY1) · 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 Q8PWY1
- Elsewhere: RCSB PDB 4CH3 · PDBe 4CH3 · UniProt Q8PWY1
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