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Crystal structure of apo DPP9

Analyse Crystal structure of apo DPP9 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7A3F
Type: protein
Length: 3,155 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dipeptidyl peptidase 9
EC: 3.4.14.5
UniProt: Q86TI2
Ligands: PO4
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 4 distinct chains · 16% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Dipeptidyl peptidase 9 (EC 3.4.14.5)	protein	782	16% helix, 33% strand	Q86TI2
A	Dipeptidyl peptidase 9 (EC 3.4.14.5)	protein	794	16% helix, 35% strand	Q86TI2
C	Dipeptidyl peptidase 9 (EC 3.4.14.5)	protein	791	16% helix, 34% strand	Q86TI2
D	Dipeptidyl peptidase 9 (EC 3.4.14.5)	protein	788	16% helix, 35% strand	Q86TI2

Ligands and binding sites

PO4 · Phosphate ion · ion · 4 copies · chains B, A, C, D
GOL · Glycerol · additive · 2 copies · chains B, A

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

Pockets

20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	216	0.84	0.97	33	empty
2	211	0.84	0.97	31	empty
3	1088	0.75	0.77	101	PO4
4	816	0.73	0.78	78	empty
5	59	0.72	0.98	16	empty

Interfaces

3 interfaces between chains.

C–D · 2237 Å² buried · 25 hydrogen bonds · protein-protein
B–A · 2167 Å² buried · 25 hydrogen bonds · protein-protein
B–C · 302 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

7A3F · Crystal structure of apo DPP9 · the same entry in another collection · chain D against D, TM-score 1.00
Q86TI2 · AlphaFold monomer V2.0 prediction for dipeptidyl peptidase 9 (Q86TI2) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 Q86TI2
Elsewhere: RCSB PDB 7A3F · PDBe 7A3F · UniProt Q86TI2

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