5ZID
Crystal Structure of human DPP-IV in complex with HL2
- PDB DOI: https://doi.org/10.2210/pdb5ZID/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Expression System: Spodoptera frugiperda
- Mutation(s): No 
- Deposited: 2018-03-14 Released: 2019-03-20 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.00 Å
- R-Value Free: 0.253 
- R-Value Work: 0.191 
- R-Value Observed: 0.194 
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 | 734 | 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
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | C | 4 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G99218JM GlyCosmos:  G99218JM GlyGen:  G99218JM |
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
9EL Query on 9EL | E [auth A], G [auth B] | (2S,3R)-2-amino-9-methoxy-3-(2,4,5-trifluorophenyl)-2,3-dihydro-1H-naphtho[2,1-b]pyran-8-carbonitrile C21 H15 F3 N2 O2 OGGAKUIGELBYAA-GHTZIAJQSA-N | |||
NAG Query on NAG | D [auth A], F [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: 3.00 Å
- R-Value Free: 0.253 
- R-Value Work: 0.191 
- R-Value Observed: 0.194 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 66.07 | α = 90 |
b = 126.19 | β = 99.3 |
c = 118.62 | γ = 90 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
MOLREP | phasing |
Entry History 
Revision History (Full details and data files)
- Version 1.0: 2019-03-20
Type: Initial release - Version 1.1: 2019-04-17
Changes: Data collection, Structure summary - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2023-11-22
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary