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Structural analysis of the tripeptide-bound form of helicobacter pylori CSD4, a D,L-carboxypeptidase

Analyse Structural analysis of the tripeptide-bound form of helicobacter pylori CSD4, a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4Q6N
Type: protein
Length: 417 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Conserved hypothetical secreted protein
UniProt: O25708
Ligands: MHI, CA
Pockets: 4 · best druggability 0.56

Structure

x-ray diffraction · 1 distinct chain · 24% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Conserved hypothetical secreted protein	protein	417	24% helix, 33% strand	O25708

Ligands and binding sites

MHI · L-ala-gamma-D-glu-meso-diaminopimelic acid · ligand · chains A
CA · Calcium ion · metal · 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	105	0.56	0.85	24	MHI, CA
2	172	0.47	0.76	28	empty
3	82	0.39	0.77	17	empty
4	60	0.27	0.73	16	empty

Compared structures

4Q6N · Structural analysis of the tripeptide-bound form of Helicobacter pylori Csd4, a… · the same entry in another collection · chain A against A, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt O25708
Elsewhere: RCSB PDB 4Q6N · PDBe 4Q6N · UniProt O25708

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