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The 1.56-ångström crystal structure of COPPER(II)-bound pqqb from pseudomonas putida
Analyse The 1.56-ångström crystal structure of COPPER(II)-bound pqqb from pseudomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Z5Y
- Type
- protein
- Length
- 308 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coenzyme pqq synthesis protein B
- UniProt
- Q88QV5
- Ligands
- ZN, CU, NA
- Pockets
- 2 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coenzyme pqq synthesis protein B | protein | 308 | 24% helix, 25% strand | Q88QV5 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
- CU · Copper (II) ion · metal · chains A
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 404 | 0.65 | 0.79 | 53 | CU |
| 2 | 93 | 0.32 | 0.73 | 16 | empty |
Compared structures
- 4Z5Y · The 1.56-angstrom crystal structure of copper(II)-bound PqqB from Pseudomonas Putida · the same entry in another collection · chain A against A, TM-score 1.00
- Q88QV5 · AlphaFold monomer V2.0 prediction for coenzyme pqq synthesis protein B (Q88QV5) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q88QV5
- Elsewhere: RCSB PDB 4Z5Y · PDBe 4Z5Y · UniProt Q88QV5
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