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Crystal structure of dipeptidyl peptidase 11 (DPP11) from porphyromonas gingivalis

Analyse Crystal structure of dipeptidyl peptidase 11 (DPP11) from porphyromonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4XZY
Type: protein
Length: 1,398 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peptidase S46
UniProt: A0A076NW73
Pockets: 10 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 51% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Peptidase S46	protein	699	51% helix, 16% strand	A0A076NW73

Ligands and binding sites

GOL · Glycerol · additive · chains A

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

Pockets

10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	840	0.72	0.77	80	GOL
2	753	0.69	0.76	75	empty
3	479	0.58	0.73	59	empty
4	54	0.51	0.87	14	empty
5	147	0.40	0.74	20	empty

Interfaces

1 interface between chains.

A–B · 899 Å² buried · 29 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

4XZY · Crystal structure of dipeptidyl peptidase 11 (DPP11) from Porphyromonas gingivalis · 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 A0A076NW73
Elsewhere: RCSB PDB 4XZY · PDBe 4XZY · UniProt A0A076NW73

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