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Structure of DPP2

Analyse Structure of DPP2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4EBB
Type: protein
Length: 899 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dipeptidyl peptidase 2
EC: 3.4.14.2
UniProt: Q9UHL4
Ligands: NAG, ZN
Pockets: 6 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 44% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Dipeptidyl peptidase 2 (EC 3.4.14.2)	protein	450	44% helix, 13% strand	Q9UHL4
B	Dipeptidyl peptidase 2 (EC 3.4.14.2)	protein	449	44% helix, 13% strand	Q9UHL4

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B
ZN · Zinc ion · metal · 3 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, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	580	0.76	0.83	52	empty
2	507	0.74	0.82	48	empty
3	173	0.55	0.80	21	empty
4	111	0.42	0.76	18	empty
5	103	0.38	0.75	17	empty

Interfaces

1 interface between chains.

A–B · 23 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 modified, 8 disulfide, 3 glycan (engineered, disulfide, N-glycosylation).

Compared structures

4EBB · Structure of DPP2 · the same entry in another collection · chain A against A, TM-score 1.00
Q9UHL4 · AlphaFold monomer V2.0 prediction for dipeptidyl peptidase 2 (Q9UHL4) · a predicted model of the same protein · 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 Q9UHL4
Elsewhere: RCSB PDB 4EBB · PDBe 4EBB · UniProt Q9UHL4

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