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

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: 4Y02
Type: protein
Length: 682 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peptidase S46
UniProt: A0A076NW73
Ligands: K
Pockets: 6 · best druggability 0.67

Structure

x-ray diffraction · 1 distinct chain · 48% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Peptidase S46	protein	682	48% helix, 16% strand	A0A076NW73

Ligands and binding sites

K · Potassium ion · metal · 2 copies · chains A
GOL · Glycerol · additive · 2 copies · chains A

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

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	585	0.67	0.77	59	K
2	362	0.59	0.76	43	K
3	61	0.45	0.83	14	GOL
4	69	0.42	0.80	20	empty
5	116	0.37	0.73	20	empty

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

4Y02 · 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 4Y02 · PDBe 4Y02 · UniProt A0A076NW73

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