MolNFT v1 · #104309 · protein

Structural analysis of the zn-form I of helicobacter pylori CSD4, a D, L-carboxypeptidase

4Q6P · Conserved hypothetical secreted protein: “Structural analysis of the zn-form I of helicobacter pylori CSD4, a D, L-carboxypeptidase”. X-ray diffraction, 3 ligands (API, ZN, CA), 4 pockets (best druggability 0.58). MolNFT v1 #104309…

PDB: 4Q6P
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: API, ZN, CA
Pockets: 4 · best druggability 0.58

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

API · 2,6-diaminopimelic acid · ligand · chains A
ZN · Zinc ion · metal · 8 copies · chains A
CA · Calcium ion · metal · 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	144	0.58	0.83	28	ZN, API
2	167	0.45	0.75	30	CA
3	115	0.39	0.74	19	empty
4	86	0.32	0.73	17	empty

Compared structures

4Q6P · Structural analysis of the Zn-form I of Helicobacter pylori Csd4, a D,L-carboxypeptidase · 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 O25708
Elsewhere: RCSB PDB 4Q6P · PDBe 4Q6P · UniProt O25708

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