MolNFT v1 · #48902 · protein
The structure of pyrrolysyl-tRNA synthetase bound to an ATP analogue
2Q7E: “The structure of pyrrolysyl-tRNA synthetase bound to an ATP analogue”. X-ray diffraction, 2 ligands (ANP, MG), 3 pockets (best druggability 0.73). MolNFT v1 #48902 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2Q7E
- Type
- protein
- Length
- 258 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyrrolysyl-tRNA synthetase
- EC
- 6.1.1.-
- UniProt
- Q8PWY1
- Ligands
- ANP, MG
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyrrolysyl-tRNA synthetase (EC 6.1.1.-) | protein | 258 | 38% helix, 24% strand | Q8PWY1 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 11 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 | 376 | 0.73 | 0.84 | 48 | MG, ANP, EDO |
| 2 | 142 | 0.42 | 0.75 | 22 | EDO |
| 3 | 73 | 0.33 | 0.75 | 13 | empty |
Compared structures
- 2Q7E · The structure of pyrrolysyl-tRNA synthetase bound to an ATP analogue · 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 0.99
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 2Q7E · PDBe 2Q7E · UniProt Q8PWY1
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