MolNFT v1 · #141064 · protein
Crystal structure of the complex of archaeal ribosomal stalk protein AP1 and archaeal ribosome recycling factor AABCE1.
5YV5 · ATPase ril: “Crystal structure of the complex of archaeal ribosomal stalk protein AP1 and archaeal ribosome recycling…”. X-ray diffraction, 2 ligands (ADP, MG), 8 pockets (best druggability 0.61). MolNFT v1 #141064 on GenesisL1: 3D…
- 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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