SAXSdb — 3q0t

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

Dipeptidyl peptidase 4

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Homooligomer	Protein 2 其他Polymer 2	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 methyl [3-(aminomethyl)-4-(2,4-dichlorophenyl)-2-methyl-7-oxo-5,7-dihydro-6H-pyrrolo[3,4-b]pyridin-6-yl]acetate × 2 water × 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 3–730； UniProt 39–766 Author chain B； PDBConstruct 3–730； 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	3q0t
Deposition date deposition_date	2010-12-16
Structure title title	Crystal structure of human dpp-iv in complex withsa-(+)- methyl2-(3-(aminomethyl)-4-(2,4-dichlorophenyl)-2-methyl- 7-oxo-5h-pyrrolo[3,4-b]pyridin-6(7h)-yl)acetate
Keywords keywords	;EXOPEPTIDASE, ALPHA/BETA HYDROLASE FOLD, BETA BARREL, BETA PROPELLER, AMINOPEPTIDASE, GLYCOPROTEIN, MEMBRANE, SERINE PROTEASE, SIGNAL-ANCHOR, TRANSMEMBRANE, 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.

3q0t__assembly_1__model_1

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

Download this curve (.dat)

3q0t__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3q0t__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.17 Å
Rg (electron density)	38.85 Å
Total Rg	39.31 Å
Atom count	12036
Residues	1454
Excluded volume	213120 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3q0t__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 (5)

Entity 1 Entity 1 polymer

Description description	Dipeptidyl peptidase 4
Molecular weight formula_weight	87450.8 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	12467

EFSRKTYTLTDYLKNTYRLKLYSLRWISDHEYLYKQENNILVFNAEYGNSSVFLENSTFDEFGHSINDYSISPDGQFILLEYNYVKQWRHSYTASYDIYDLNKRQLITEERIPNNTQWVTWSPVGHKLAYVWNNDIYVKIEPNLPSYRITWTGKEDIIYNGITDWVYEEEVFSAYSALWWSPNGTFLAYAQFNDTEVPLIEYSFYSDESLQYPKTVRVPYPKAGAVNPTVKFFVVNTDSLSSVTNATSIQITAPASMLIGDHYLCDVTWATQERISLQWLRRIQNYSVMDICDYDESSGRWNCLVARQHIEMSTTGWVGRFRPSEPHFTLDGNSFYKIISNEEGYRHICYFQIDKKDCTFITKGTWEVIGIEALTSDYLYYISNEYKGMPGGRNLYKIQLSDYTKVTCLSCELNPERCQYYSVSFSKEAKYYQLRCSGPGLPLYTLHSSVNDKGLRVLEDNSALDKMLQNVQMPSKKLDFIILNETKFWYQMILPPHFDKSKKYPLLLDVYAGPCSQKADTVFRLNWATYLASTENIIVASFDGRGSGYQGDKIMHAINRRLGTFEVEDQIEAARQFSKMGFVDNKRIAIWGWSYGGYVTSMVLGSGSGVFKCGIAVAPVSRWEYYDSVYTERYMGLPTPEDNLDHYRNSTVMSRAENFKQVEYLLIHGTADDNVHFQQSAQISKALVDVGVDFQAMWYTDEDHGIASSTAHQHIYTHMSHFIKQCFSLPPLEQKLISEEDLNSAVDHHHHHH

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Pichia pastoris

Entity 2 Entity 2 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	10

Entity 4 Entity 4 non-polymer

Description description	methyl [3-(aminomethyl)-4-(2,4-dichlorophenyl)-2-methyl-7-oxo-5,7-dihydro-6H-pyrrolo[3,4-b]pyridin-6-yl]acetate
Molecular weight formula_weight	394.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	431

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3q0ta1
Class class	b — All beta proteins
Fold Fold fold	b.70 — 8-bladed beta-propeller
Superfamily Superfamily superfamily	b.70.3 — DPP6 N-terminal domain-like
Family Family family	b.70.3.1 — DPP6 N-terminal domain-like

Domain ID domain_id	d3q0ta2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
Family Family family	c.69.1.24 — DPP6 catalytic domain-like

Domain ID domain_id	d3q0tb1
Class class	b — All beta proteins
Fold Fold fold	b.70 — 8-bladed beta-propeller
Superfamily Superfamily superfamily	b.70.3 — DPP6 N-terminal domain-like
Family Family family	b.70.3.1 — DPP6 N-terminal domain-like

Domain ID domain_id	d3q0tb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
Family Family family	c.69.1.24 — DPP6 catalytic domain-like

CATH v4.4 (4 domains)

Domain ID domain_id	3q0tA01
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	3q0tA02
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	3q0tB01
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	3q0tB02
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	65.686 Å
Unit-cell length b length_b	67.569 Å
Unit-cell length c length_c	420.978 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.401 Å
Low-resolution limit resolution_low	47.952 Å
R factor r_factor	0.2046
R_work r_work	0.2023
R_free r_free	0.2604

Crystal structure of human dpp-iv in complex withsa-(+)- methyl2-(3-(aminomethyl)-4-(2,4-dichlorophenyl)-2-methyl- 7-oxo-5h-pyrrolo[3,4-b]pyridin-6(7h)-yl)acetate

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

Dipeptidyl peptidase 4

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

3q0t__assembly_1__model_1

3q0t__assembly_1__model_1 | I(q)

3q0t__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of human dpp-iv in complex withsa-(+)- methyl2-(3-(aminomethyl)-4-(2,4-dichlorophenyl)-2-methyl- 7-oxo-5h-pyrrolo[3,4-b]pyridin-6(7h)-yl)acetate

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

Dipeptidyl peptidase 4

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

3q0t__assembly_1__model_1

3q0t__assembly_1__model_1 | I(q)

3q0t__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)