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Crystal structure of cell shape determinant protein CSD4 GLN46HIS variant from helicobacter pylori

Analyse Crystal structure of cell shape determinant protein CSD4 GLN46HIS variant from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4WCM
Type: protein
Length: 415 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, IOD, PO4
Pockets: 4 · best druggability 0.54

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	415	25% helix, 33% strand	B5ZAD9

Ligands and binding sites

API · 2,6-diaminopimelic acid · ligand · chains A
ZN · Zinc ion · metal · 4 copies · chains A
IOD · Iodide ion · ion · 37 copies · chains A
PO4 · Phosphate ion · ion · 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	90	0.54	0.85	22	PO4, API
2	167	0.47	0.76	27	IOD
3	96	0.36	0.74	21	IOD
4	62	0.31	0.75	17	empty

Compared structures

4WCM · Crystal Structure of Cell Shape Determinant protein Csd4 Gln46His variant from… · 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 4WCM · PDBe 4WCM · UniProt B5ZAD9

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