3CCB
Crystal Structure of Human DPP4 in complex with a benzimidazole derivative
- PDB DOI: https://doi.org/10.2210/pdb3CCB/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Expression System: Spodoptera frugiperda
- Mutation(s): No 
- Deposited: 2008-02-25 Released: 2008-10-21 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.49 Å
- R-Value Free: 0.244 
- R-Value Work: 0.200 
- R-Value Observed: 0.202 
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 | 740 | 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 | |
NAG Query on NAG | J [auth A] K [auth A] L [auth A] M [auth A] O [auth B] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
B2Y Query on B2Y | N [auth A], S [auth B], V [auth C], Y [auth D] | 1-biphenyl-2-ylmethanamine C13 H13 N YHXKXVFQHWJYOD-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.49 Å
- R-Value Free: 0.244 
- R-Value Work: 0.200 
- R-Value Observed: 0.202 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 122.086 | α = 90 |
b = 123.01 | β = 114.84 |
c = 144.651 | γ = 90 |
Software Name | Purpose |
---|---|
DENZO | data reduction |
SCALEPACK | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
Entry History 
Deposition Data
- Released Date: 2008-10-21  Deposition Author(s): Wallace, M.B., Skene, R.J.
Revision History (Full details and data files)
- Version 1.0: 2008-10-21
Type: Initial release - Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance - Version 1.2: 2017-10-25
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