1WCY

Crystal Structure Of Human Dipeptidyl Peptidase IV (DPPIV) Complex With Diprotin A

PDB DOI: https://doi.org/10.2210/pdb1WCY/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2004-05-07 Released: 2005-05-07
Deposition Author(s): Hiramatsu, H., Yamamoto, A., Kyono, K., Higashiyama, Y., Fukushima, C., Shima, H., Sugiyama, S., Inaka, K., Shimizu, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.265
R-Value Work: 0.224

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.2 of the entry. See complete history.

Literature

The crystal structure of human dipeptidyl peptidase IV (DPPIV) complex with diprotin A

Hiramatsu, H., Yamamoto, A., Kyono, K., Higashiyama, Y., Fukushima, C., Shima, H., Sugiyama, S., Inaka, K., Shimizu, R.

(2004) Biol Chem 385: 561-564

PubMed: 15255191 Search on PubMed
DOI: https://doi.org/10.1515/BC.2004.068
Primary Citation of Related Structures:
1WCY

PubMed Abstract:
Dipeptidyl peptidase IV (DPPIV) is a serine protease, a member of the prolyl oligopeptidase (POP) family, and has been implicated in several diseases. Therefore, it seems important to develop selective inhibitors for human DPPIV (hDPPIV) that are able to control the biological function of hDPPIV. In order to elucidate the binding mode and substrate specificity, we determined the crystal structure complex of hDPPIV and diprotin A (IIe-Pro-IIe), a slowly hydrolyzed substrate of hDPPIV, at 2.2 A resolution. In this paper, we discuss the molecular interaction mechanism of diprotin A with hDPPIV based on the X-ray crystal structure.

Organizational Affiliation

Tanabe Seiyaku Co. Ltd., 3-16-89 Kashima, Yodogawa-ku, Osaka 532-8505, Japan.

Macromolecule Content

Total Structure Weight: 176.41 kDa
Atom Count: 13,485
Modelled Residue Count: 1,464
Deposited Residue Count: 1,486
Unique protein chains: 2

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	740	Homo sapiens	Mutation(s): 0 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
Glycosylation
Glycosylation Sites: 6	Glycosylation Focus chain A Focus chain B	Go to GlyGen: P27487-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Diprotin A	C, D	3	N/A	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

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

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F, G, H, J, K	2		N-Glycosylation	Interactions Focus chain F Focus chain G Focus chain H Focus chain J Focus chain K
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain N [auth B] SDF format, chain P [auth B] SDF format, chain M [auth A] SDF format, chain O [auth B] MOL2 format, chain L [auth A] MOL2 format, chain N [auth B] MOL2 format, chain P [auth B] MOL2 format, chain M [auth A] MOL2 format, chain O [auth B] mmCIF format, chain L [auth A] mmCIF format, chain N [auth B] mmCIF format, chain P [auth B] mmCIF format, chain M [auth A] mmCIF format, chain O [auth B]	L [auth A], M [auth A], N [auth B], O [auth B], P [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.265
R-Value Work: 0.224
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.02	α = 90
b = 126.06	β = 90
c = 136.67	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
CNX	refinement
CCP4	data scaling
CNX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2005-05-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-05-07
Type: Initial release
Version 1.1: 2008-04-30
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: Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2023-10-25
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-11-06
Changes: Structure summary