6HP8 | pdb_00006hp8

Crystal structure of DPP8 in complex with Val-BoroPro

PDB DOI: https://doi.org/10.2210/pdb6HP8/pdb

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

Deposited: 2018-09-19 Released: 2019-07-31
Deposition Author(s): Ross, B.H., Huber, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.228 (Depositor), 0.229 (DCC)
R-Value Work:
0.203 (Depositor), 0.206 (DCC)
R-Value Observed:
0.205 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Improvement of Protein Crystal Diffraction Using Post-Crystallization Methods: Infrared Laser Radiation Controls Crystal Order

Ross, B.H.

(2019) Thesis

Macromolecule Content

Total Structure Weight: 312.54 kDa
Atom Count: 21,265
Modeled Residue Count: 2,508
Deposited Residue Count: 2,694
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidyl peptidase 8	A, B, C	898	Homo sapiens	Mutation(s): 0 Gene Names: DPP8, DPRP1, MSTP097, MSTP135, MSTP141 EC: 3.4.14.5
UniProt & NIH Common Fund Data Resources
Find proteins for Q6V1X1 (Homo sapiens) Explore Q6V1X1 Go to UniProtKB: Q6V1X1
PHAROS: Q6V1X1 GTEx: ENSG00000074603
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6V1X1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GK2 (Subject of Investigation/LOI) Query on GK2 Download Ideal Coordinates CCD File SDF format, chain R [auth C] SDF format, chain K [auth B] SDF format, chain D [auth A] MOL2 format, chain R [auth C] MOL2 format, chain K [auth B] MOL2 format, chain D [auth A] mmCIF format, chain R [auth C] mmCIF format, chain K [auth B] mmCIF format, chain D [auth A]	D [auth A], K [auth B], R [auth C]	[(2~{R})-1-[(2~{R})-2-azanyl-3-methyl-butanoyl]pyrrolidin-2-yl]boronic acid C₉ H₁₉ B N₂ O₃ FKCMADOPPWWGNZ-JGVFFNPUSA-N		Interactions Focus chain D [auth A] Focus chain K [auth B] Focus chain R [auth C] Interactions & Density Focus chain D [auth A] Focus chain K [auth B] Focus chain R [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain X [auth C] SDF format, chain W [auth C] SDF format, chain V [auth C] SDF format, chain U [auth C] SDF format, chain T [auth C] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain X [auth C] MOL2 format, chain W [auth C] MOL2 format, chain V [auth C] MOL2 format, chain U [auth C] MOL2 format, chain T [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain X [auth C] mmCIF format, chain W [auth C] mmCIF format, chain V [auth C] mmCIF format, chain U [auth C] mmCIF format, chain T [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] H [auth A] I [auth A] J [auth A] F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], T [auth C], U [auth C], V [auth C], W [auth C], X [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain S [auth C] SDF format, chain L [auth B] SDF format, chain E [auth A] MOL2 format, chain S [auth C] MOL2 format, chain L [auth B] MOL2 format, chain E [auth A] mmCIF format, chain S [auth C] mmCIF format, chain L [auth B] mmCIF format, chain E [auth A]	E [auth A], L [auth B], S [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Focus chain S [auth C] Interactions & Density Focus chain E [auth A] Focus chain L [auth B] Focus chain S [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.228 (Depositor), 0.229 (DCC)
R-Value Work: 0.203 (Depositor), 0.206 (DCC)
R-Value Observed: 0.205 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 163.163	α = 90
b = 245.317	β = 90
c = 261.588	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2019-07-31

Deposition Author(s):

Ross, B.H.

Huber, R.

Revision History (Full details and data files)

Version 1.0: 2019-07-31
Type: Initial release
Version 1.1: 2024-11-13
Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary