6Y0F

Structure of human FAPalpha in complex with linagliptin

• PDB DOI: https://doi.org/10.2210/pdb6Y0F/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera aff. frugiperda 1 BOLD-2017
• Mutation(s): No 


• Deposited: 2020-02-07 Released: 2021-02-17 
• Deposition Author(s): Nar, H., Schnapp, G., Schreiner, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.92 Å
• R-Value Free: 0.243 
• R-Value Work: 0.207 
• R-Value Observed: 0.208 

Starting Model: experimental

Literature

Structure of human FAPalpha in complex with linagliptin

Nar, H., Schnapp, G., Schreiner, P.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 341.54 kDa 
• Atom Count: 24,077 
• Modelled Residue Count: 2,882 
• Deposited Residue Count: 2,888 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prolyl endopeptidase FAP	A, B, C, D	722	Homo sapiens	Mutation(s): 0  Gene Names: FAP EC: 3.4.21.26 (PDB Primary Data), 3.4.14.5 (PDB Primary Data), 3.4.21 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q12884 (Homo sapiens) Explore Q12884  Go to UniProtKB:  Q12884
PHAROS:  Q12884 GTEx:  ENSG00000078098
Glycosylation
Glycosylation Sites: 4		Go to GlyGen: Q12884-1

Oligosaccharides

Help

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	E, G, H, I, J	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	K, L, M	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G86851RC GlyCosmos:  G86851RC GlyGen:  G86851RC

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
356 (Subject of Investigation/LOI)	Q [auth A], S [auth B], U [auth C], W [auth D]	8-[(3R)-3-Aminopiperidin-1-yl]-7-but-2-yn-1-yl-3-methyl-1-[(4-methylquinazolin-2-yl)methyl]-3,7-dihydro-1H-purine-2,6-d ione C25 H28 N8 O2 LTXREWYXXSTFRX-QGZVFWFLSA-N
NAG	N [auth A], O [auth A], P [auth A], R [auth B], T [auth C], V [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.92 Å
• R-Value Free: 0.243 
• R-Value Work: 0.207 
• R-Value Observed: 0.208 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.586	α = 90
b = 253.604	β = 89.76
c = 115.247	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
BUSTER	refinement
PDB_EXTRACT	data extraction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-02-17 
Deposition Author(s): Nar, H., Schnapp, G., Schreiner, P.

Revision History  

• Version 1.0: 2021-02-17
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary