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Structure of helicobacter pylori CSD3 from the hexagonal crystal

Analyse Structure of helicobacter pylori CSD3 from the hexagonal crystal in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4RNZ
Type: protein
Length: 359 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Conserved hypothetical secreted protein
UniProt: O25247
Ligands: NI, ZN, PO4
Pockets: 4 · best druggability 0.67

Structure

x-ray diffraction · 1 distinct chain · 19% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Conserved hypothetical secreted protein	protein	359	19% helix, 41% strand	O25247

Ligands and binding sites

NI · Nickel (II) ion · metal · 2 copies · chains A
ZN · Zinc ion · metal · chains A
PO4 · Phosphate ion · ion · 3 copies · chains A
GOL · Glycerol · additive · 3 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

4 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	413	0.67	0.80	50	empty
2	99	0.48	0.81	17	empty
3	137	0.42	0.75	31	empty
4	70	0.42	0.81	20	empty

Compared structures

4RNZ · Structure of Helicobacter pylori Csd3 from the hexagonal crystal · 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 O25247
Elsewhere: RCSB PDB 4RNZ · PDBe 4RNZ · UniProt O25247

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