4WJL
Structure of human dipeptidyl peptidase 10 (DPPY): a modulator of neuronal Kv4 channels
- PDB DOI: https://doi.org/10.2210/pdb4WJL/pdb
- Classification: MEMBRANE PROTEIN
- Organism(s): Homo sapiens
- Expression System: Spodoptera frugiperda
- Mutation(s): Yes 
- Deposited: 2014-09-30 Released: 2015-03-18 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.40 Å
- R-Value Free: 0.242 
- R-Value Work: 0.207 
- R-Value Observed: 0.209 
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Inactive dipeptidyl peptidase 10 | 719 | Homo sapiens | Mutation(s): 2  Gene Names: DPP10, DPRP3, KIAA1492 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q8N608 (Homo sapiens) Explore Q8N608  Go to UniProtKB:  Q8N608 | |||||
PHAROS:  Q8N608 GTEx:  ENSG00000175497  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q8N608 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | C | 4 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G81315DD GlyCosmos:  G81315DD GlyGen:  G81315DD |
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | H [auth A], I [auth A], J [auth B], K [auth B] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.40 Å
- R-Value Free: 0.242 
- R-Value Work: 0.207 
- R-Value Observed: 0.209 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 80.91 | α = 90 |
b = 143.73 | β = 90 |
c = 176.25 | γ = 90 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
SCALA | data scaling |
PHASER | phasing |
PDB_EXTRACT | data extraction |
iMOSFLM | data reduction |
Entry History 
Deposition Data
- Released Date: 2015-03-18  Deposition Author(s): Bezerra, G.A., Dobrovetsky, E., Seitova, A., Fedosyuk, S., Dhe-Paganon, S., Gruber, K.
Revision History (Full details and data files)
- Version 1.0: 2015-03-18
Type: Initial release - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary