Research workbench

DPP8 bound to a dipeptide (mp) from the N-terminus of BRCA2

Analyse DPP8 bound to a dipeptide (mp) from the N-terminus of BRCA2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6QZW
Type: protein
Length: 2,505 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dipeptidyl peptidase 8; Met-pro
EC: 3.4.14.5
UniProt: Q6V1X1
Ligands: NA
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 18% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C, A, B	Dipeptidyl peptidase 8 (EC 3.4.14.5)	protein	833	18% helix, 35% strand	Q6V1X1
D, E, F	Met-pro	protein	2	0% helix, 0% strand	—

Ligands and binding sites

NA · Sodium ion · metal · chains C

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

Pockets

20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	138	0.81	0.98	30	empty
2	629	0.81	0.86	60	empty
3	684	0.81	0.85	70	empty
4	1126	0.80	0.81	87	empty
5	154	0.80	0.96	33	empty

Interfaces

5 interfaces between chains.

A–B · 2388 Å² buried · 32 hydrogen bonds · protein-protein
C–A · 413 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 267 Å² buried · 11 hydrogen bonds · protein-protein
B–E · 262 Å² buried · 12 hydrogen bonds · protein-protein
C–F · 258 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

6QZW · DPP8 bound to a dipeptide (MP) from the N-terminus of BRCA2 · the same entry in another collection · chain C against C, TM-score 1.00
Q6V1X1 · AlphaFold monomer V2.0 prediction for dipeptidyl peptidase 8 (Q6V1X1) · 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 Q6V1X1
Elsewhere: RCSB PDB 6QZW · PDBe 6QZW · UniProt Q6V1X1

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