MolNFT v1 · #184908 · protein
Cryo-EM structure of the hexameric RUVBL1-RUVBL2 in complex with ZNHIT2
7P6X · Ruvb-like 1: “Cryo-EM structure of the hexameric RUVBL1-RUVBL2 in complex with ZNHIT2”. Electron microscopy, 1 ligand (ADP), 20 pockets (best druggability 0.86). MolNFT v1 #184908 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7P6X
- Type
- protein
- Length
- 1,813 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- 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 · 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 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 Q9Y265
- Every structure of UniProt Q9Y230
- Elsewhere: RCSB PDB 7P6X · PDBe 7P6X · UniProt Q9Y265 · UniProt Q9Y230
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