3JYH

Human dipeptidyl peptidase DPP7

PDB DOI: https://doi.org/10.2210/pdb3JYH/pdb

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

Deposited: 2009-09-21 Released: 2009-10-13
Deposition Author(s): Dobrovetsky, E., Dong, A., Seitova, A., Crombett, L., Paganon, S., Cossar, D., Edwards, A.M., Arrowsmith, C.H., Bountra, C., Weigelt, J., Hassel, A., Shewchuk, L., Bochkarev, A., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free:
0.222 (Depositor), 0.223 (DCC)
R-Value Work:
0.180 (Depositor), 0.180 (DCC)
R-Value Observed:
0.182 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Human dipeptidyl peptidase DPP7

Dobrovetsky, E., Dong, A., Seitova, A., Crombett, L., Paganon, S., Cossar, D., Edwards, A.M., Arrowsmith, C.H., Bountra, C., Weigelt, J., Hassel, A., Shewchuk, L., Bochkarev, A.

To be published.

Macromolecule Content

Total Structure Weight: 213.38 kDa
Atom Count: 15,144
Modelled Residue Count: 1,805
Deposited Residue Count: 1,876
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidyl-peptidase 2	A, B, C, D	469	Homo sapiens	Mutation(s): 0 Gene Names: DPP2, DPP7, QPP EC: 3.4.14.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UHL4 (Homo sapiens) Explore Q9UHL4 Go to UniProtKB: Q9UHL4
PHAROS: Q9UHL4 GTEx: ENSG00000176978
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UHL4
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D	Go to GlyGen: Q9UHL4-1
Sequence Annotations Expand
Reference Sequence LOADING

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, G, I	3		N-Glycosylation	Interactions Focus chain E Focus chain G Focus chain I Interactions & Density Focus chain E Focus chain G Focus chain I
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F, H, J, K, L	2		N-Glycosylation	Interactions Focus chain F Focus chain H Focus chain J Focus chain K Focus chain L Interactions & Density Focus chain F Focus chain H Focus chain J Focus chain K Focus chain L
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth D] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth D] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth D]	M [auth A] N [auth A] O [auth B] P [auth C] Q [auth C] M [auth A], N [auth A], O [auth B], P [auth C], Q [auth C], R [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth D] Interactions & Density Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free: 0.222 (Depositor), 0.223 (DCC)
R-Value Work: 0.180 (Depositor), 0.180 (DCC)
R-Value Observed: 0.182 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.216	α = 90
b = 130.215	β = 102.36
c = 124.436	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
DENZO	data reduction
HKL-3000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-10-13

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2009-10-13
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2024-11-20
Changes: Data collection, Database references, Structure summary