MolNFT v1 · #147819 · protein

DPP8 - slrflyeg, space group 20

6EOP · Dipeptidyl peptidase 8: “DPP8 - slrflyeg, space group 20”. X-ray diffraction, 2 ligands (F15, CA), 20 pockets (best druggability 0.86). MolNFT v1 #147819 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6EOP
Type: protein
Length: 2,540 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dipeptidyl peptidase 8; Ser-leu-arg-phe-leu-tyr-glu-gly
EC: 3.4.14.5
UniProt: Q6V1X1
Ligands: F15, CA
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 4 distinct chains · 19% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Dipeptidyl peptidase 8 (EC 3.4.14.5)	protein	841	19% helix, 35% strand	Q6V1X1
B	Dipeptidyl peptidase 8 (EC 3.4.14.5)	protein	838	19% helix, 35% strand	Q6V1X1
C	Dipeptidyl peptidase 8 (EC 3.4.14.5)	protein	837	19% helix, 35% strand	Q6V1X1
D, E, F	Ser-leu-arg-phe-leu-tyr-glu-gly	protein	8	0% helix, 13% strand	—

Ligands and binding sites

F15 · Pentadecanoic acid · ligand · 3 copies · chains A, D, B, E, C, F
CA · Calcium ion · metal · 3 copies · chains A, B, C
FLC · Citrate anion · additive · chains 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, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	693	0.86	0.90	82	F15
2	885	0.85	0.87	84	F15
3	1074	0.84	0.85	96	F15
4	457	0.81	0.89	54	empty
5	597	0.80	0.86	55	empty

Interfaces

5 interfaces between chains.

B–C · 2465 Å² buried · 29 hydrogen bonds · protein-protein
B–E · 896 Å² buried · 15 hydrogen bonds · protein-protein
A–D · 874 Å² buried · 19 hydrogen bonds · protein-protein
C–F · 867 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 538 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 modified (artifact).

Compared structures

6EOP · DPP8 - SLRFLYEG, space group 20 · the same entry in another collection · chain F against F, TM-score 1.00
Q6V1X1 · AlphaFold monomer V2.0 prediction for dipeptidyl peptidase 8 (Q6V1X1) · a predicted model of the same protein · chain B 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 6EOP · PDBe 6EOP · UniProt Q6V1X1

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.