MolNFT v1 · #111938 · protein

The 1.56-ångström crystal structure of COPPER(II)-bound pqqb from pseudomonas putida

4Z5Y · Coenzyme pqq synthesis protein B: “The 1.56-ångström crystal structure of COPPER(II)-bound pqqb from pseudomonas putida”. X-ray diffraction, 3 ligands (ZN, CU, NA), 2 pockets (best druggability 0.65). MolNFT v1 #111938 on GenesisL1…

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.

Pocket	Volume (Å³)	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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