Research workbench

Crystal structure of product bound cell shape determinant protein CSD4 from helicobacter pylori

Analyse Crystal structure of product bound cell shape determinant protein CSD4 from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4WCL
Type: protein
Length: 416 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Conserved hypothetical secreted protein
UniProt: B5ZAD9
Ligands: API, ZN, NA, IOD
Pockets: 4 · best druggability 0.53

Structure

x-ray diffraction · 1 distinct chain · 25% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Conserved hypothetical secreted protein	protein	416	25% helix, 33% strand	B5ZAD9

Ligands and binding sites

API · 2,6-diaminopimelic acid · ligand · chains A
ZN · Zinc ion · metal · 3 copies · chains A
NA · Sodium ion · metal · chains A
IOD · Iodide ion · ion · 31 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	106	0.53	0.83	25	API
2	91	0.36	0.74	17	IOD
3	67	0.33	0.76	16	empty
4	71	0.32	0.75	16	IOD

Compared structures

4WCL · Crystal Structure of product bound Cell Shape Determinant protein Csd4 from Helicobacter… · 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 B5ZAD9
Elsewhere: RCSB PDB 4WCL · PDBe 4WCL · UniProt B5ZAD9

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.