6RN6

DPP1 in complex with inhibitor

• PDB DOI: https://doi.org/10.2210/pdb6RN6/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2019-05-08 Released: 2019-08-28 
• Deposition Author(s): Kack, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.221 
• R-Value Work: 0.174 
• R-Value Observed: 0.176 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 80.19 kDa 
• Atom Count: 5,755 
• Modelled Residue Count: 688 
• Deposited Residue Count: 702 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidyl peptidase 1	A, D	119	Homo sapiens	Mutation(s): 0  Gene Names: CTSC, CPPI EC: 3.4.14.1
UniProt & NIH Common Fund Data Resources
Find proteins for P53634 (Homo sapiens) Explore P53634  Go to UniProtKB:  P53634
PHAROS:  P53634 GTEx:  ENSG00000109861

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidyl peptidase 1	B, E	163	Homo sapiens	Mutation(s): 0  Gene Names: CTSC, CPPI EC: 3.4.14.1
UniProt & NIH Common Fund Data Resources
Find proteins for P53634 (Homo sapiens) Explore P53634  Go to UniProtKB:  P53634
PHAROS:  P53634 GTEx:  ENSG00000109861

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidyl peptidase 1	C, F	69	Homo sapiens	Mutation(s): 0  Gene Names: CTSC, CPPI EC: 3.4.14.1
UniProt & NIH Common Fund Data Resources
Find proteins for P53634 (Homo sapiens) Explore P53634  Go to UniProtKB:  P53634
PHAROS:  P53634 GTEx:  ENSG00000109861

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K9Q	O [auth E]	(2~{S},4~{R})-~{N}-[(2~{S})-1-azanyl-3-(4-phenylphenyl)propan-2-yl]-4-oxidanyl-pyrrolidine-2-carboxamide C20 H25 N3 O2 WUFQVJYTXQDLCX-OTWHNJEPSA-N
NAG	G [auth A], H [auth A], J [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL	I [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	K [auth B], L [auth B], M [auth B], N [auth C], P [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.221 
• R-Value Work: 0.174 
• R-Value Observed: 0.176 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.591	α = 90
b = 84.591	β = 90
c = 223.385	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-08-28 
Deposition Author(s): Kack, H.

Revision History  

• Version 1.0: 2019-08-28
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description, Structure summary