Research workbench
Cryo-Em structure of the hexameric RUVBL1-RUVBL2 in complex with ZNHIT2
Analyse Cryo-Em structure of the hexameric RUVBL1-RUVBL2 in complex with ZNHIT2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7P6X
- Type
- protein
- Length
- 1,813 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 4.1
- Source
- Homo sapiens
- Molecule
- RuvB-like 1; RuvB-like 2
- EC
- 3.6.4.12
- UniProt
- Q9Y265, Q9Y230
- Ligands
- ADP
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · resolution 4.1 · 6 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RuvB-like 1 (EC 3.6.4.12) | protein | 320 | 48% helix, 17% strand | Q9Y265 |
| B | RuvB-like 1 (EC 3.6.4.12) | protein | 313 | 48% helix, 16% strand | Q9Y265 |
| C | RuvB-like 1 (EC 3.6.4.12) | protein | 322 | 46% helix, 17% strand | Q9Y265 |
| D | RuvB-like 2 (EC 3.6.4.12) | protein | 282 | 52% helix, 13% strand | Q9Y230 |
| E | RuvB-like 2 (EC 3.6.4.12) | protein | 288 | 51% helix, 15% strand | Q9Y230 |
| F | RuvB-like 2 (EC 3.6.4.12) | protein | 288 | 51% helix, 15% strand | Q9Y230 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1193 | 0.86 | 0.87 | 126 | ADP |
| 2 | 1070 | 0.85 | 0.86 | 113 | ADP |
| 3 | 1148 | 0.84 | 0.85 | 115 | ADP |
| 4 | 1121 | 0.78 | 0.80 | 92 | empty |
| 5 | 1145 | 0.74 | 0.77 | 114 | empty |
Interfaces
7 interfaces between chains.
- A–F · 1952 Ų buried · 11 hydrogen bonds · protein-protein
- C–F · 1918 Ų buried · 10 hydrogen bonds · protein-protein
- B–E · 1853 Ų buried · 9 hydrogen bonds · protein-protein
- C–E · 1838 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 1744 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 7P6X · Cryo-EM structure of the hexameric RUVBL1-RUVBL2 in complex with ZNHIT2 · the same entry in another collection · chain F against F, TM-score 1.00
- Q9Y230 · AlphaFold monomer V2.0 prediction for ruvb-like 2 (Q9Y230) · a predicted model of the same protein · chain D against A, TM-score 0.97
- Q9Y265 · AlphaFold monomer V2.0 prediction for ruvb-like 1 (Q9Y265) · a predicted model of the same protein · chain B against A, TM-score 0.94
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 Q9Y265
- Every structure of UniProt Q9Y230
- Elsewhere: RCSB PDB 7P6X · PDBe 7P6X · UniProt Q9Y265 · UniProt Q9Y230
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