3QBJ
Crystal structure of dipeptidyl peptidase IV in complex with inhibitor
- PDB DOI: https://doi.org/10.2210/pdb3QBJ/pdb
- Classification: hydrolase/hydrolase inhibitor
- Organism(s): Homo sapiens
- Expression System: Spodoptera frugiperda
- Mutation(s): Yes 
- Deposited: 2011-01-13 Released: 2012-01-25 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.21 Å
- R-Value Free: 0.235 
- R-Value Work: 0.202 
- R-Value Observed: 0.203 
This is version 2.0 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 | 748 | Homo sapiens | Mutation(s): 2  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
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | C, E | 2 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT |
Entity ID: 3 | |||||
---|---|---|---|---|---|
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 | D | 4 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G81315DD GlyCosmos:  G81315DD GlyGen:  G81315DD |
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NXZ Query on NXZ | H [auth A], J [auth B] | 1-[(3S,4S)-4-amino-1-(6-phenylpyrimidin-4-yl)pyrrolidin-3-yl]piperidin-2-one C19 H23 N5 O FHAABBQZMYZFKY-RDJZCZTQSA-N | |||
NAG Query on NAG | F [auth A], G [auth A], I [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: 2.21 Å
- R-Value Free: 0.235 
- R-Value Work: 0.202 
- R-Value Observed: 0.203 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 65.751 | α = 90 |
b = 69.082 | β = 90 |
c = 424.16 | γ = 90 |
Software Name | Purpose |
---|---|
SCALA | data scaling |
BUSTER-TNT | refinement |
PDB_EXTRACT | data extraction |
XSCALE | data scaling |
BUSTER | refinement |
Entry History 
Deposition Data
- Released Date: 2012-01-25  Deposition Author(s): Liu, S.P.
Revision History (Full details and data files)
- Version 1.0: 2012-01-25
Type: Initial release - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary