Research workbench
Crystal structure of the C-terminal domain of ifrs bound with 3-iodo- L-phe and ATP
Analyse Crystal structure of the C-terminal domain of ifrs bound with 3-iodo- L-phe and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4TQD
- 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, 33S, MG
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyrrolysine--tRNA ligase (EC 6.1.1.26) | protein | 258 | 39% helix, 23% strand | Q8PWY1 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- 33S · 3-iodo-L-phenylalanine · ligand · chains A
- MG · Magnesium ion · metal · 3 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
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 418 | 0.71 | 0.82 | 40 | MG, ATP, 33S |
| 2 | 82 | 0.32 | 0.73 | 17 | empty |
| 3 | 58 | 0.27 | 0.73 | 13 | empty |
| 4 | 50 | 0.26 | 0.73 | 11 | empty |
Compared structures
- 4TQD · Crystal Structure of the C-terminal domain of IFRS bound with 3-iodo-L-Phe and ATP · 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 4TQD · PDBe 4TQD · UniProt Q8PWY1
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