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3o9v

Crystal Structure of Human DPP4 Bound to TAK-986

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Dipeptidyl peptidase 4

Homo sapiens

UniProt P27487

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Other combination Homooligomer Protein 4 其他Polymer 5 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 5 5-(aminomethyl)-2-methyl-4-(4-methylphenyl)-6-(2-methylpropyl)pyridine-3-carboxic acid × 4 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 water × 4 Consistent with protein count
2 Other combination Homooligomer Protein 2 其他Polymer 3 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 5-(aminomethyl)-2-methyl-4-(4-methylphenyl)-6-(2-methylpropyl)pyridine-3-carboxic acid × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 water × 2 Consistent with protein count
3 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 5-(aminomethyl)-2-methyl-4-(4-methylphenyl)-6-(2-methylpropyl)pyridine-3-carboxic acid × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
2bub 2bub

2 assemblies

Homodimer
1j2e 1nu6 1pfq 1rwq 2ajl 2g5p 2g5t 2g63 2g63 2i03 2i03 2i78

44 assemblies; showing the first 12

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1n1m 1nu8 1r9m 1r9m 1r9m 1r9m 1r9n 1r9n 1r9n 1tk3 1tkr 1u8e

124 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name DPP4_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 13–740； UniProt 39–766 Author chain B； PDBConstruct 13–740； UniProt 39–766 Author chain C； PDBConstruct 13–740； UniProt 39–766 Author chain D； PDBConstruct 13–740； 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_id3o9v
Deposition date deposition_date2010-08-04
Structure title titleCrystal Structure of Human DPP4 Bound to TAK-986
Keywords keywords;protease and 8-bladed beta-propeller domain, Aminopeptidase, Cell membrane, Glycoprotein, Hydrolase, Membrane, Protease, Secreted, Serine protease, Signal-anchor, Transmembrane, SIGNALING PROTEIN, SIGNALING PROTEIN-INHIBITOR complex ;; HYDROLASE,SIGNALING PROTEIN/INHIBITOR
Experimental Method methodX-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.

3o9v__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3o9v__assembly_2__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

3o9v__assembly_2__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）39.31 Å
Rg (electron density)38.90 Å
Total Rg39.41 Å
Atom count12184
Residues1460
Excluded volume215820 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3o9v__assembly_1__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3o9v__assembly_2__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 3o9v__assembly_3__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)

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6. Fold Classification (SCOP + CATH) 17 domains

SCOP 2.08 (9 domains)

Domain ID domain_idd3o9va1
Class classb — All beta proteins
Fold Fold foldb.70 — 8-bladed beta-propeller
Superfamily Superfamily superfamilyb.70.3 — DPP6 N-terminal domain-like
Family Family familyb.70.3.1 — DPP6 N-terminal domain-like
Domain ID domain_idd3o9va2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamilyc.69.1 — alpha/beta-Hydrolases
Family Family familyc.69.1.0 — automated matches
Domain ID domain_idd3o9vb1
Class classb — All beta proteins
Fold Fold foldb.70 — 8-bladed beta-propeller
Superfamily Superfamily superfamilyb.70.3 — DPP6 N-terminal domain-like
Family Family familyb.70.3.1 — DPP6 N-terminal domain-like
Domain ID domain_idd3o9vb2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamilyc.69.1 — alpha/beta-Hydrolases
Family Family familyc.69.1.0 — automated matches
Domain ID domain_idd3o9vb3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3o9vc1
Class classb — All beta proteins
Fold Fold foldb.70 — 8-bladed beta-propeller
Superfamily Superfamily superfamilyb.70.3 — DPP6 N-terminal domain-like
Family Family familyb.70.3.1 — DPP6 N-terminal domain-like
Domain ID domain_idd3o9vc2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamilyc.69.1 — alpha/beta-Hydrolases
Family Family familyc.69.1.0 — automated matches
Domain ID domain_idd3o9vd1
Class classb — All beta proteins
Fold Fold foldb.70 — 8-bladed beta-propeller
Superfamily Superfamily superfamilyb.70.3 — DPP6 N-terminal domain-like
Family Family familyb.70.3.1 — DPP6 N-terminal domain-like
Domain ID domain_idd3o9vd2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamilyc.69.1 — alpha/beta-Hydrolases
Family Family familyc.69.1.0 — automated matches

CATH v4.4 (8 domains)

Domain ID domain_id3o9vA01
Class class2 — Mainly Beta
Architecture architecture140 — 8 Propeller
Topology topology10 — Methanol Dehydrogenase; Chain A
Homologous superfamily homologous superfamily30 — Dipeptidylpeptidase IV, N-terminal domain
Domain ID domain_id3o9vA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1820 — Alpha/Beta hydrolase fold, catalytic domain
Domain ID domain_id3o9vB01
Class class2 — Mainly Beta
Architecture architecture140 — 8 Propeller
Topology topology10 — Methanol Dehydrogenase; Chain A
Homologous superfamily homologous superfamily30 — Dipeptidylpeptidase IV, N-terminal domain
Domain ID domain_id3o9vB02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1820 — Alpha/Beta hydrolase fold, catalytic domain
Domain ID domain_id3o9vC01
Class class2 — Mainly Beta
Architecture architecture140 — 8 Propeller
Topology topology10 — Methanol Dehydrogenase; Chain A
Homologous superfamily homologous superfamily30 — Dipeptidylpeptidase IV, N-terminal domain
Domain ID domain_id3o9vC02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1820 — Alpha/Beta hydrolase fold, catalytic domain
Domain ID domain_id3o9vD01
Class class2 — Mainly Beta
Architecture architecture140 — 8 Propeller
Topology topology10 — Methanol Dehydrogenase; Chain A
Homologous superfamily homologous superfamily30 — Dipeptidylpeptidase IV, N-terminal domain
Domain ID domain_id3o9vD02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1820 — Alpha/Beta hydrolase fold, catalytic domain
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7. Citations (1)