MolNFT v1 · #106798 · protein
Crystal structure of the C-terminal domain of ifrs bound with 2-(5- bromothienyl)-L-ala and ATP
4TQF · Pyrrolysine--tRNA ligase: “Crystal structure of the C-terminal domain of ifrs bound with 2-(5- bromothienyl)-L-ala and ATP”. X-ray diffraction, 3 ligands (ATP, 33W, MG), 3 pockets (best druggability 0.71). MolNFT v1 #106798 on…
- PDB
- 4TQF
- Type
- protein
- Length
- 258 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
- ATP, 33W, MG
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyrrolysine--tRNA ligase (EC 6.1.1.26) | protein | 258 | 37% helix, 23% strand | Q8PWY1 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- 33W · 3-(5-bromothiophen-2-yl)-L-alanine · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 7 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 | 454 | 0.71 | 0.81 | 46 | MG, ATP, 33W |
| 2 | 89 | 0.34 | 0.74 | 19 | empty |
| 3 | 55 | 0.28 | 0.74 | 14 | empty |
Compared structures
- 4TQF · Crystal Structure of the C-terminal domain of IFRS bound with 2-(5-bromothienyl)-L-Ala… · 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 4TQF · PDBe 4TQF · UniProt Q8PWY1
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