2ONC
Crystal structure of human DPP-4
- PDB DOI: https://doi.org/10.2210/pdb2ONC/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Expression System: Spodoptera frugiperda
- Mutation(s): No 
- Deposited: 2007-01-23 Released: 2008-03-04 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.55 Å
- R-Value Free: 0.254 
- R-Value Work: 0.195 
- R-Value Observed: 0.198 
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 |
Dipeptidyl peptidase 4 | 731 | Homo sapiens | Mutation(s): 0  Gene Names: DPP4, ADCP2, CD26 EC: 3.4.14.5 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P27487 (Homo sapiens) Explore P27487  Go to UniProtKB:  P27487 | |||||
PHAROS:  P27487 GTEx:  ENSG00000197635  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P27487 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
SY1 Query on SY1 | AA [auth C] DA [auth D] EA [auth D] N [auth A] O [auth A] | 2-({2-[(3R)-3-AMINOPIPERIDIN-1-YL]-4-OXOQUINAZOLIN-3(4H)-YL}METHYL)BENZONITRILE C21 H21 N5 O OYNURZXTLNNKAP-QGZVFWFLSA-N | |||
NAG Query on NAG | BA [auth D] CA [auth D] J [auth A] K [auth A] L [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.55 Å
- R-Value Free: 0.254 
- R-Value Work: 0.195 
- R-Value Observed: 0.198 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 122.357 | α = 90 |
b = 123.702 | β = 114.89 |
c = 145.358 | γ = 90 |
Software Name | Purpose |
---|---|
DENZO | data reduction |
SCALEPACK | data scaling |
MOLREP | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
ADSC | data collection |
HKL-2000 | data reduction |
Entry History 
Deposition Data
- Released Date: 2008-03-04  Deposition Author(s): Feng, J., Zhang, Z., Wallace, M.B., Stafford, J.A., Kaldor, S.W., Kassel, D.B., Navre, M., Shi, L., Skene, R.J., Asakawa, T., Takeuchi, K., Xu, R., Webb, D.R., Gwaltney, S.L.
Revision History (Full details and data files)
- Version 1.0: 2008-03-04
Type: Initial release - Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance - Version 1.2: 2017-10-18
Changes: Refinement description - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary - Version 2.1: 2023-12-27
Changes: Data collection, Database references, Structure summary