Research workbench
Conformational changes in the catalytic domain of the cpx-ATPase copb-B upon nucleotide binding
Analyse Conformational changes in the catalytic domain of the cpx-ATPase copb-B upon… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YJ6
- Type
- protein
- Length
- 500 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Copper-transporting ATPase
- EC
- 3.6.1.36, 3.6.3.10
- UniProt
- Q97UU7
- Ligands
- A99, PO4
- Pockets
- 7 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Copper-transporting ATPase (EC 3.6.1.36, 3.6.3.10) | protein | 248 | 33% helix, 27% strand | Q97UU7 |
| B | Copper-transporting ATPase (EC 3.6.1.36, 3.6.3.10) | protein | 252 | 33% helix, 27% strand | Q97UU7 |
Ligands and binding sites
- A99 · 5'-O-[(S)-hydroxy{[(R)-hydroxy({(S)-hydroxy[(1S)-1-(2-nitrophenyl)ethoxy]phosphoryl}oxy)phosphoryl]oxy}phosphoryl]adenosine · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 224 | 0.68 | 0.85 | 31 | empty |
| 2 | 73 | 0.66 | 0.92 | 16 | empty |
| 3 | 366 | 0.57 | 0.75 | 47 | A99 |
| 4 | 385 | 0.56 | 0.74 | 41 | empty |
| 5 | 82 | 0.45 | 0.81 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 560 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2YJ6 · Conformational changes in the catalytic domain of the CPx-ATPase CopB- B upon nucleotide… · 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 Q97UU7
- Elsewhere: RCSB PDB 2YJ6 · PDBe 2YJ6 · UniProt Q97UU7
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