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Structure of dpp III from saccharomyces cerevisiae

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

PDB: 3CSK
Type: protein
Length: 710 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Probable dipeptidyl-peptidase 3
EC: 3.4.14.4
UniProt: Q08225
Ligands: MG, ZN
Pockets: 7 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 48% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Probable dipeptidyl-peptidase 3 (EC 3.4.14.4)	protein	710	48% helix, 15% strand	Q08225

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains A
ZN · Zinc ion · metal · chains A

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

Pockets

7 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	765	0.76	0.81	89	empty
2	288	0.57	0.77	36	empty
3	94	0.52	0.83	19	empty
4	144	0.51	0.80	26	empty
5	161	0.47	0.76	27	empty

Compared structures

3CSK · Structure of DPP III from Saccharomyces cerevisiae · the same entry in another collection · chain A against A, TM-score 1.00
Q08225 · AlphaFold monomer V2.0 prediction for probable dipeptidyl peptidase 3 (Q08225) · a predicted model of the same protein · chain A against A, TM-score 0.74

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 Q08225
Elsewhere: RCSB PDB 3CSK · PDBe 3CSK · UniProt Q08225

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