1NU8

Crystal structure of human dipeptidyl peptidase IV (DPP-IV) in complex with Diprotin A (IPI)

PDB DOI: https://doi.org/10.2210/pdb1NU8/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens, synthetic construct
Expression System: Komagataella pastoris
Mutation(s): No

Deposited: 2003-01-31 Released: 2003-08-26
Deposition Author(s): Thoma, R., Loeffler, B., Stihle, M., Huber, W., Ruf, A., Hennig, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.282
R-Value Work: 0.225
R-Value Observed: 0.225

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 171.04 kDa
Atom Count: 12,335
Modelled Residue Count: 1,459
Deposited Residue Count: 1,459
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	728	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
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
3-mer peptide	C [auth D]	3	synthetic construct	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

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 D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth B] D [auth A], E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], J [auth B], K [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.282
R-Value Work: 0.225
R-Value Observed: 0.225
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.136	α = 90
b = 67.067	β = 90
c = 419.635	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CCP4	model building
REFMAC	refinement
CCP4	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2003-08-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2003-08-26
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 1.3: 2016-08-24
Changes: Structure summary
Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Data collection, Derived calculations, Structure summary

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1NU8

Crystal structure of human dipeptidyl peptidase IV (DPP-IV) in complex with Diprotin A (IPI)

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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