5LLS

Porcine dipeptidyl peptidase IV in complex with 8-(3-aminopiperidin-1-yl)-7-[(2-bromophenyl)methyl]-1,3-dimethyl-2,3,6,7-tetrahydro-1H-purine-2,6-dione

PDB DOI: https://doi.org/10.2210/pdb5LLS/pdb

Classification: HYDROLASE
Organism(s): Sus scrofa
Mutation(s): No

Deposited: 2016-07-28 Released: 2016-09-14
Deposition Author(s): Nar, H., Blaesse, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.41 Å
R-Value Free: 0.228
R-Value Work: 0.190
R-Value Observed: 0.192

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 364.43 kDa
Atom Count: 25,567
Modelled Residue Count: 2,908
Deposited Residue Count: 3,064
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidyl peptidase 4	A, B, C, D	766	Sus scrofa	Mutation(s): 0 EC: 3.4.14.5
UniProt
Find proteins for P22411 (Sus scrofa) Explore P22411 Go to UniProtKB: P22411
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P22411
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, F, G, H, I E, F, G, H, I, J, K, L, M	2		N-Glycosylation	Interactions Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M Interactions & Density Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6Z8 Query on 6Z8 Download Ideal Coordinates CCD File SDF format, chain LA [auth D] SDF format, chain R [auth A] SDF format, chain AA [auth B] SDF format, chain GA [auth C] SDF format, chain IA [auth C] SDF format, chain NA [auth D] SDF format, chain T [auth A] SDF format, chain Y [auth B] MOL2 format, chain LA [auth D] MOL2 format, chain R [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain GA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain NA [auth D] MOL2 format, chain T [auth A] MOL2 format, chain Y [auth B]	AA [auth B] GA [auth C] IA [auth C] LA [auth D] NA [auth D] AA [auth B], GA [auth C], IA [auth C], LA [auth D], NA [auth D], R [auth A], T [auth A], Y [auth B]	8-[(3~{R})-3-azanylpiperidin-1-yl]-7-[(2-bromophenyl)methyl]-1,3-dimethyl-purine-2,6-dione C₁₉ H₂₃ Br N₆ O₂ CADOMWLQFMIXFQ-CYBMUJFWSA-N		Interactions Focus chain AA [auth B] Focus chain GA [auth C] Focus chain IA [auth C] Focus chain LA [auth D] Focus chain NA [auth D] Focus chain R [auth A] Focus chain T [auth A] Focus chain Y [auth B] Interactions & Density Focus chain AA [auth B] Focus chain GA [auth C] Focus chain IA [auth C] Focus chain LA [auth D] Focus chain NA [auth D] Focus chain R [auth A] Focus chain T [auth A] Focus chain Y [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain FA [auth C] SDF format, chain W [auth B] SDF format, chain BA [auth C] SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain JA [auth D] SDF format, chain KA [auth D] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain X [auth B] MOL2 format, chain CA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain W [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain JA [auth D] MOL2 format, chain KA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain X [auth B]	BA [auth C] CA [auth C] DA [auth C] EA [auth C] FA [auth C] BA [auth C], CA [auth C], DA [auth C], EA [auth C], FA [auth C], JA [auth D], KA [auth D], N [auth A], O [auth A], P [auth A], Q [auth A], U [auth B], V [auth B], W [auth B], X [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain HA [auth C] SDF format, chain MA [auth D] SDF format, chain S [auth A] MOL2 format, chain Z [auth B] MOL2 format, chain HA [auth C] MOL2 format, chain MA [auth D] MOL2 format, chain S [auth A]	HA [auth C], MA [auth D], S [auth A], Z [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain HA [auth C] Focus chain MA [auth D] Focus chain S [auth A] Focus chain Z [auth B] Interactions & Density Focus chain HA [auth C] Focus chain MA [auth D] Focus chain S [auth A] Focus chain Z [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.41 Å
R-Value Free: 0.228
R-Value Work: 0.190
R-Value Observed: 0.192
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.9	α = 112.7
b = 117.68	β = 94.6
c = 133.12	γ = 91.2

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling
CNX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-09-14

Deposition Author(s):

Nar, H.

Blaesse, M.

Revision History (Full details and data files)

Version 1.0: 2016-09-14
Type: Initial release
Version 1.1: 2019-10-16
Changes: Data collection
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-01-10
Changes: Data collection, Database references, Refinement description, Structure summary