Research workbench
Crystal structure of archaeal L7AE bound to eukaryotic kink-loop
Analyse Crystal structure of archaeal L7AE bound to eukaryotic kink-loop in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OZQ
- Type
- protein + RNA
- Length
- 616 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 50S ribosomal protein L7AE; RNA
- UniProt
- Q8U160
- Ligands
- NA, CA, CL
- Pockets
- 11 · best druggability 0.65
Structure
x-ray diffraction · 5 distinct chains · 50% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | 50S ribosomal protein L7AE | protein | 123 | 50% helix, 15% strand | Q8U160 |
| B | 50S ribosomal protein L7AE | protein | 122 | 49% helix, 16% strand | Q8U160 |
| D | 50S ribosomal protein L7AE | protein | 121 | 51% helix, 16% strand | Q8U160 |
| E, G, H | RNA | rna | 32 | — | — |
| F | RNA | rna | 31 | — | — |
Ligands and binding sites
- NA · Sodium ion · metal · 6 copies · chains E, F, G
- CA · Calcium ion · metal · 3 copies · chains E, F
- CL · Chloride ion · ion · chains H
- ACT · Acetate ion · additive · 5 copies · chains B, G, E, F, D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 493 | 0.65 | 0.77 | 57 | ACT |
| 2 | 462 | 0.60 | 0.75 | 44 | empty |
| 3 | 207 | 0.51 | 0.77 | 22 | NA |
| 4 | 202 | 0.48 | 0.76 | 23 | ACT |
| 5 | 180 | 0.44 | 0.74 | 23 | empty |
Interfaces
11 interfaces between chains.
- D–G · 652 Ų buried · 23 hydrogen bonds · protein-nucleic
- C–F · 631 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–H · 625 Ų buried · 21 hydrogen bonds · protein-nucleic
- B–E · 604 Ų buried · 17 hydrogen bonds · protein-nucleic
- B–D · 323 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 7OZQ · Crystal structure of archaeal L7Ae bound to eukaryotic kink-loop · the same entry in another collection · chain C against C, TM-score 1.00
- Q8U160 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L7AE (Q8U160) · a predicted model of the same protein · chain D 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 Q8U160
- Elsewhere: RCSB PDB 7OZQ · PDBe 7OZQ · UniProt Q8U160
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.