4FFW | pdb_00004ffw

Crystal Structure of Dipeptidyl Peptidase IV (DPP4, DPP-IV, CD26) in Complex with Fab + sitagliptin

PDB DOI: https://doi.org/10.2210/pdb4FFW/pdb

Classification: HYDROLASE/Immune System, INHIBITOR
Organism(s): Rattus norvegicus, Mus musculus
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2012-06-01 Released: 2012-12-12
Deposition Author(s): Wang, Z., Sudom, A., Walker, N.P., Min, X.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.311 (Depositor), 0.310 (DCC)
R-Value Work:
0.287 (Depositor), 0.286 (DCC)
R-Value Observed:
0.288 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

An Inhibitory Antibody Against DPP IV Improves Glucose Tolerance in vivo - Validation of Large Molecule Approach for DPP IV Inhibition

Tang, J., Majeti, J., Sudom, A., Xiong, Y., Lu, M., Liu, Q., Higbee, J., Zhang, Y., Wang, Y., Wang, W., Cao, P., Xia, Z., Johnstone, S., Yang, X., Yu, T., Sharkov, N., Walker, N., Tu, H., Shen, W., Wang, Z.

To be published.

Macromolecule Content

Total Structure Weight: 261.89 kDa
Atom Count: 18,266
Modeled Residue Count: 2,282
Deposited Residue Count: 2,314
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidyl peptidase 4	A, B	730	Rattus norvegicus	Mutation(s): 0 Gene Names: Dpp4, Cd26 EC: 3.4.14.5
UniProt
Find proteins for P14740 (Rattus norvegicus) Explore P14740 Go to UniProtKB: P14740
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P14740
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab light chain	C, F [auth L]	210	Mus musculus	Mutation(s): 0

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab heavy chain	D, E [auth H]	217	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
715 Query on 715 Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain G [auth A]	G [auth A], H [auth B]	(2R)-4-OXO-4-[3-(TRIFLUOROMETHYL)-5,6-DIHYDRO[1,2,4]TRIAZOLO[4,3-A]PYRAZIN-7(8H)-YL]-1-(2,4,5-TRIFLUOROPHENYL)BUTAN-2-A MINE C₁₆ H₁₅ F₆ N₅ O MFFMDFFZMYYVKS-SECBINFHSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
715	BindingDB: 4FFW	IC50: 26.01 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.311 (Depositor), 0.310 (DCC)
R-Value Work: 0.287 (Depositor), 0.286 (DCC)
R-Value Observed: 0.288 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.77	α = 90
b = 200.86	β = 93.64
c = 97.93	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-12-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-12-12
Type: Initial release
Version 1.1: 2018-06-06
Changes: Data collection
Version 1.2: 2021-05-19
Changes: Derived calculations, Source and taxonomy, Structure summary
Version 1.3: 2024-11-06
Changes: Data collection, Database references, Structure summary