1ORV

Crystal Structure of Porcine Dipeptidyl Peptidase IV (CD26)

PDB DOI: https://doi.org/10.2210/pdb1ORV/pdb

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

Deposited: 2003-03-16 Released: 2003-05-06
Deposition Author(s): Engel, M., Hoffmann, T., Wagner, L., Wermann, M., Heiser, U., Kiefersauer, R., Huber, R., Bode, W., Demuth, H.U., Brandstetter, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.252
R-Value Work: 0.217
R-Value Observed: 0.217

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 345.56 kDa
Atom Count: 25,836
Modelled Residue Count: 2,912
Deposited Residue Count: 2,912
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 IV	A, B, C, D	728	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, H, I, K E, F, H, I, K, L, M	2		N-Glycosylation	Interactions Focus chain E Focus chain F Focus chain H Focus chain I Focus chain K Focus chain L Focus chain M Interactions & Density Focus chain E Focus chain F Focus chain H Focus chain I Focus chain K Focus chain L Focus chain M
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	G, J	3		N-Glycosylation	Interactions Focus chain G Focus chain J Interactions & Density Focus chain G Focus chain J
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain EA [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 S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain Z [auth C] SDF format, chain DA [auth D] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain EA [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 S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain DA [auth D]	AA [auth C] BA [auth C] DA [auth D] EA [auth D] N [auth A] AA [auth C], BA [auth C], DA [auth D], EA [auth D], N [auth A], O [auth A], P [auth A], Q [auth A], S [auth B], T [auth B], U [auth B], V [auth B], X [auth C], Y [auth C], Z [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain FA [auth D] SDF format, chain R [auth A] SDF format, chain W [auth B] MOL2 format, chain CA [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain R [auth A] MOL2 format, chain W [auth B]	CA [auth C], FA [auth D], R [auth A], W [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain CA [auth C] Focus chain FA [auth D] Focus chain R [auth A] Focus chain W [auth B] Interactions & Density Focus chain CA [auth C] Focus chain FA [auth D] Focus chain R [auth A] Focus chain W [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.252
R-Value Work: 0.217
R-Value Observed: 0.217
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62	α = 112.76
b = 118.18	β = 94.93
c = 133.59	γ = 91.14

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
MAIN	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2003-05-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2003-05-06
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary