Research workbench
Crystal structure of the complex of archaeal ribosomal stalk protein AP1 and archaeal ribosome recycling factor AABCE1.
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
- 5YV5
- Type
- protein
- Length
- 531 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATPase ril; Archaeal ribosomal stalk protein AP1
- UniProt
- I6V0C7
- Ligands
- ADP, MG
- Pockets
- 8 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATPase ril | protein | 517 | 37% helix, 21% strand | I6V0C7 |
| B | Archaeal ribosomal stalk protein AP1 | protein | 14 | 79% helix, 0% strand | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 399 | 0.61 | 0.77 | 58 | empty |
| 2 | 188 | 0.53 | 0.78 | 24 | empty |
| 3 | 161 | 0.43 | 0.74 | 24 | empty |
| 4 | 139 | 0.42 | 0.75 | 22 | ADP, MG |
| 5 | 103 | 0.40 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 587 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5YV5 · 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
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 I6V0C7
- Elsewhere: RCSB PDB 5YV5 · PDBe 5YV5 · UniProt I6V0C7
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