2qt9

Human dipeptidyl peptidase iv/cd26 in complex with a 4-aryl cyclohexylalanine inhibitor

Method: X-RAY DIFFRACTION Dmax: 127.8 Å Quality: GOOD

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

Dipeptidyl peptidase 4

Homo sapiens

UniProt P27487

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Homooligomer Protein × 2 其他Polymer 9 PDB declaration: undecameric(11) Consistent with all polymer counts Chain A; UniProt 1–766 Chain B; UniProt 1–766 Mutation:T39S 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 7 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 NA SODIUM ION × 1 524 (2S,3S)-3-AMINO-4-[(3S)-3-FLUOROPYRROLIDIN-1-YL]-N,N-DIMETHYL-4-OXO-2-(TRANS-4-[1,2,4]TRIAZOLO[1,5-A]PYRIDIN-5-YLCYCLOH EXYL)BUTANAMIDE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;293 K;PEG4000, Sodium Acetate, TRIS, pH 8.0, vapor diffusion, hanging drop, temperature 293K, pH 8.000000, VAPOR DIFFUSION, HANGING DROP Resolution 2.10 Å R-free 0.229

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

113 other PDB entries and 169 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DPP4_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–766; UniProt 1–766 Author chain B; PDBConstruct 1–766; UniProt 1–766

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.

SAXS scattering curve SAXS Profile

SAXS profile for 2qt9

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2qt9
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id2qt9
Deposition date deposition_date2007-08-01
Structure title titleHuman dipeptidyl peptidase iv/cd26 in complex with a 4-aryl cyclohexylalanine inhibitor
Keywords keywords;ALPHA/BETA, BETA-PROPELLER, DIMER, Aminopeptidase, Glycoprotein, Hydrolase, Membrane, Protease, Secreted, Serine protease, Signal-anchor, Transmembrane ;; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier39.31
Radius of gyration Rg (electron density) rg_electron38.94
Forward intensity I(0) i0446107000.00
Molecular weight molecular_weight174530.0 kDa
Excluded volume excluded_volume218530 ų
Envelope volume envelope_volume284460 ų
Hydration-shell volume shell_volume59899 ų
Envelope diameter envelope_diameter132.3
Shell Rg shell_rg45.74
Envelope Rg envelope_rg38.63
Shape Rg shape_rg38.89
Total Rg total_rg39.47
Total atoms total_atoms12329
Residues n_residues1456
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax127.8
Rg (real space) rg_real39.33
Rg uncertainty (real space) rg_real_error1.02
I(0) (real space) i0_real4.4610e+08
I(0) uncertainty (real space) i0_real_error7.1990e+06
Rg (reciprocal space) rg_reciprocal39.32
I(0) (reciprocal space) i0_reciprocal446100000.0000
Solution quality estimate total_estimate0.8834
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary41.5
Skewness Skewness skewness0.339
Kurtosis Kurtosis kurtosis-0.519
Angular range angular_range— – 0.2000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha53390000.0000
Real-space data points n_real_points41
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.869; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.876

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd2qt9a1
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_idd2qt9a2
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_idd2qt9b1
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_idd2qt9b2
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 (4 domains)

Domain ID domain_id2qt9A01
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_id2qt9A02
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_id2qt9B01
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_id2qt9B02
Class class2 — Mainly Beta
Architecture architecture140 — 8 Propeller
Topology topology10 — Methanol Dehydrogenase; Chain A
Homologous superfamily homologous superfamily30 — Dipeptidylpeptidase IV, N-terminal domain

8. Citations (1)

9. Files and Curves (10)