Research workbench
Crystal structure of the complex of archaeal ribosomal stalk protein AP1 and archaeal translation initiation factor AIF5B
Analyse Crystal structure of the complex of archaeal ribosomal stalk protein AP1 and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YT0
- Type
- protein
- Length
- 342 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable translation initiation factor if-2; Archaeal ribosomal stalk protein AP1
- UniProt
- Q9Y9B3
- Ligands
- GDP
- Pockets
- 1 · best druggability 0.46
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable translation initiation factor if-2 | protein | 331 | 34% helix, 30% strand | Q9Y9B3 |
| B | Archaeal ribosomal stalk protein AP1 | protein | 11 | 36% helix, 0% strand | — |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 149 | 0.46 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 694 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5YT0 · Crystal structure of the complex of archaeal ribosomal stalk protein aP1 and archaeal… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y9B3 · AlphaFold monomer V2.0 prediction for probable translation initiation factor if-2 (Q9Y9B3) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q9Y9B3
- Elsewhere: RCSB PDB 5YT0 · PDBe 5YT0 · UniProt Q9Y9B3
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