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Human dipeptidyl peptidase DPP7

Analyse Human dipeptidyl peptidase DPP7 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3JYH
Type: protein
Length: 1,805 residues
Chains: 4
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, BMA
Pockets: 15 · best druggability 0.78

Structure

x-ray diffraction · 3 distinct chains · 44% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Dipeptidyl-peptidase 2 (EC 3.4.14.2)	protein	452	45% helix, 13% strand	Q9UHL4
C	Dipeptidyl-peptidase 2 (EC 3.4.14.2)	protein	451	43% helix, 13% strand	Q9UHL4
D	Dipeptidyl-peptidase 2 (EC 3.4.14.2)	protein	450	45% helix, 13% strand	Q9UHL4

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 22 copies · chains A, B, C, D
BMA · beta-D-mannopyranose · sugar · 3 copies · chains A, B, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	80	0.78	0.99	17	empty
2	71	0.76	0.99	16	empty
3	455	0.73	0.82	46	empty
4	454	0.72	0.82	44	empty
5	430	0.72	0.82	45	empty

Interfaces

3 interfaces between chains.

C–D · 2205 Å² buried · 29 hydrogen bonds · protein-protein
A–B · 2191 Å² buried · 27 hydrogen bonds · protein-protein
A–C · 338 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide, 14 glycan (disulfide, N-glycosylation).

Compared structures

3JYH · Human dipeptidyl peptidase DPP7 · the same entry in another collection · chain D against D, 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 3JYH · PDBe 3JYH · UniProt Q9UHL4

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