MolNFT v2 · #227951 · protein
RUVBL1/2 in complex with ATP
9EMC · RuvB-like 1: “RUVBL1/2 in complex with ATP”. Electron microscopy at 3.26, 2 ligands (ATP, MG), 20 pockets (best druggability 0.84). MolNFT v2 #227951 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 9EMC
- Type
- protein
- Length
- 1,977 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.26
- Source
- Homo sapiens
- Molecule
- RuvB-like 1; RuvB-like 2
- EC
- 3.6.4.12
- UniProt
- Q9Y265, Q9Y230
- Ligands
- ATP, MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · resolution 3.26 · 2 distinct chains · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | RuvB-like 1 (EC 3.6.4.12) | protein | 322 | 46% helix, 18% strand | Q9Y265 |
| D, F, E | RuvB-like 2 (EC 3.6.4.12) | protein | 337 | 45% helix, 18% strand | Q9Y230 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 6 copies · chains A, F, D, B, C, E
- MG · Magnesium ion · metal · 6 copies · chains A, F, D, B, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 302 | 0.84 | 0.95 | 40 | ATP, MG |
| 2 | 310 | 0.84 | 0.94 | 43 | ATP, MG |
| 3 | 271 | 0.84 | 0.95 | 44 | ATP, MG |
| 4 | 277 | 0.84 | 0.95 | 46 | ATP, MG |
| 5 | 293 | 0.84 | 0.94 | 37 | ATP, MG |
Interfaces
12 interfaces between chains.
- A–D · 3303 Ų buried · 42 hydrogen bonds · protein-protein
- C–F · 3294 Ų buried · 41 hydrogen bonds · protein-protein
- B–E · 3279 Ų buried · 42 hydrogen bonds · protein-protein
- D–B · 3026 Ų buried · 33 hydrogen bonds · protein-protein
- C–E · 3025 Ų buried · 34 hydrogen bonds · protein-protein
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 9EMC · PDBe 9EMC · UniProt Q9Y265 · UniProt Q9Y230
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