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.

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

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structure of human FAPalpha in complex with linagliptin

Nar, H., Schnapp, G., Schreiner, P.

To be published.

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

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q12884
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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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	Interactions Focus chain E Focus chain G Focus chain H Focus chain I Focus chain J Interactions & Density Focus chain E Focus chain G Focus chain H Focus chain I Focus chain J
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	Interactions Focus chain F Interactions & Density Focus chain F
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	Interactions Focus chain K Focus chain L Focus chain M Interactions & Density Focus chain K Focus chain L Focus chain M
Glycosylation Resources
GlyTouCan: G86851RC GlyCosmos: G86851RC GlyGen: G86851RC

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
356 (Subject of Investigation/LOI) Query on 356 Download Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain S [auth B] SDF format, chain U [auth C] SDF format, chain W [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain S [auth B] MOL2 format, chain U [auth C] MOL2 format, chain W [auth D]	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		Interactions Focus chain Q [auth A] Focus chain S [auth B] Focus chain U [auth C] Focus chain W [auth D] Interactions & Density Focus chain Q [auth A] Focus chain S [auth B] Focus chain U [auth C] Focus chain W [auth D]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain R [auth B] SDF format, chain T [auth C] SDF format, chain V [auth D] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain R [auth B] MOL2 format, chain T [auth C] MOL2 format, chain V [auth D]	N [auth A] O [auth A] P [auth A] R [auth B] T [auth C] 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		Interactions Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain R [auth B] Focus chain T [auth C] Focus chain V [auth D] Interactions & Density Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain R [auth B] Focus chain T [auth C] Focus chain V [auth D]