Research workbench
Model of ribosome-bound archaeal pelota and ABCE1
Analyse Model of ribosome-bound archaeal pelota and ABCE1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3J15
- Type
- protein
- Length
- 950 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein pelota; ABC transporter ATP-binding protein
- EC
- 3.1.-.-
- UniProt
- Q5JIB9
- Ligands
- ADP, SF4
- Pockets
- 14 · best druggability 0.69
Structure
electron microscopy · 2 distinct chains · 33% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein pelota (EC 3.1.-.-) | protein | 357 | 34% helix, 20% strand | Q5JIB9 |
| B | ABC transporter ATP-binding protein | protein | 593 | 33% helix, 20% strand | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains B
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 769 | 0.69 | 0.76 | 71 | ADP |
| 2 | 97 | 0.61 | 0.87 | 21 | empty |
| 3 | 315 | 0.57 | 0.77 | 35 | ADP |
| 4 | 208 | 0.44 | 0.73 | 23 | empty |
| 5 | 121 | 0.42 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 367 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 disulfide (covalent ligand, disulfide).
Compared structures
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 Q5JIB9
- Elsewhere: RCSB PDB 3J15 · PDBe 3J15 · UniProt Q5JIB9
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