SAXSdb — 4pv7

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Dipeptidyl peptidase 4 soluble form

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	1-[2-(2,4-dichlorophenyl)-1-(methylsulfonyl)-1H-indol-3-yl]methanamine × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DPP4_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 25–752； UniProt 39–766 Author chain B； PDBConstruct 25–752； UniProt 39–766

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4pv7
Deposition date deposition_date	2014-03-15
Structure title title	Cocrystal structure of dipeptidyl-peptidase 4 with an indole scaffold inhibitor
Keywords keywords	Beta-Propeller, Hydrolase, extrocellular side, HYDROLASE-HYDROLASE INHIBITOR complex; HYDROLASE/HYDROLASE INHIBITOR
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

4pv7__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4pv7__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4pv7__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	39.15 Å
Rg (electron density)	38.85 Å
Total Rg	39.33 Å
Atom count	11948
Residues	1454
Excluded volume	211670 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4pv7__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Dipeptidyl peptidase 4 soluble form
Molecular weight formula_weight	87295.6 kDa
EC 编号 ec_number	3.4.14.5
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	11948

HHHHHHDYDIPTTENLYFQGAMGSSRKTYTLTDYLKNTYRLKLYSLRWISDHEYLYKQENNILVFNAEYGNSSVFLENSTFDEFGHSINDYSISPDGQFILLEYNYVKQWRHSYTASYDIYDLNKRQLITEERIPNNTQWVTWSPVGHKLAYVWNNDIYVKIEPNLPSYRITWTGKEDIIYNGITDWVYEEEVFSAYSALWWSPNGTFLAYAQFNDTEVPLIEYSFYSDESLQYPKTVRVPYPKAGAVNPTVKFFVVNTDSLSSVTNATSIQITAPASMLIGDHYLCDVTWATQERISLQWLRRIQNYSVMDICDYDESSGRWNCLVARQHIEMSTTGWVGRFRPSEPHFTLDGNSFYKIISNEEGYRHICYFQIDKKDCTFITKGTWEVIGIEALTSDYLYYISNEYKGMPGGRNLYKIQLSDYTKVTCLSCELNPERCQYYSVSFSKEAKYYQLRCSGPGLPLYTLHSSVNDKGLRVLEDNSALDKMLQNVQMPSKKLDFIILNETKFWYQMILPPHFDKSKKYPLLLDVYAGPCSQKADTVFRLNWATYLASTENIIVASFDGRGSGYQGDKIMHAINRRLGTFEVEDQIEAARQFSKMGFVDNKRIAIWGWSYGGYVTSMVLGSGSGVFKCGIAVAPVSRWEYYDSVYTERYMGLPTPEDNLDHYRNSTVMSRAENFKQVEYLLIHGTADDNVHFQQSAQISKALVDVGVDFQAMWYTDEDHGIASSTAHQHIYTHMSHFIKQCFSLP

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	SPODOPTERA FRUGIPERDA

Entity 2 Entity 2 non-polymer

Description description	1-[2-(2,4-dichlorophenyl)-1-(methylsulfonyl)-1H-indol-3-yl]methanamine
Molecular weight formula_weight	369.3 kDa
Source method src_method	syn
Copy count entity_count	2

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	4pv7A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	4pv7A02
Class class	2 — Mainly Beta
Architecture architecture	140 — 8 Propeller
Topology topology	10 — Methanol Dehydrogenase; Chain A
Homologous superfamily homologous superfamily	30 — Dipeptidylpeptidase IV, N-terminal domain

Domain ID domain_id	4pv7B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	4pv7B02
Class class	2 — Mainly Beta
Architecture architecture	140 — 8 Propeller
Topology topology	10 — Methanol Dehydrogenase; Chain A
Homologous superfamily homologous superfamily	30 — Dipeptidylpeptidase IV, N-terminal domain

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Unit-cell length a length_a	79.815 Å
Unit-cell length b length_b	79.815 Å
Unit-cell length c length_c	286.756 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 32
Space-group number int_tables_number	145
Crystal system crystal_system	—

Resolution resolution	3.240 Å
Low-resolution limit resolution_low	49.750 Å
R factor r_factor	0.2249
R_work r_work	0.2232
R_free r_free	0.2640

Cocrystal structure of dipeptidyl-peptidase 4 with an indole scaffold inhibitor

1. Protein Identity and Related Structures Protein Identity & Related Structures

Dipeptidyl peptidase 4 soluble form

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4pv7__assembly_1__model_1

4pv7__assembly_1__model_1 | I(q)

4pv7__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Cocrystal structure of dipeptidyl-peptidase 4 with an indole scaffold inhibitor

1. Protein Identity and Related Structures Protein Identity & Related Structures

Dipeptidyl peptidase 4 soluble form

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4pv7__assembly_1__model_1

4pv7__assembly_1__model_1 | I(q)

4pv7__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)