7svl

DPP9 IN COMPLEX WITH LIGAND ICeD-2

Method: X-RAY DIFFRACTION Dmax: 190.8 Å Quality: GOOD

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

Dipeptidyl peptidase 9

Homo sapiens

UniProt Q86TI2

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1–863 Chain B; UniProt 1–863 Not recorded D06 (2S)-2-amino-1-(1,3-dihydro-2H-isoindol-2-yl)-2-[(1r,4S)-4-(pyrrolidin-1-yl)cyclohexyl]ethan-1-one × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;293 K;10% PEG 8000 25% Glycerol 0.16 M Calcium Acetate 0.08 M Cacodilate pH 6.25 Resolution 2.46 Å R-free 0.341
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 1–863 Chain D; UniProt 1–863 Not recorded D06 (2S)-2-amino-1-(1,3-dihydro-2H-isoindol-2-yl)-2-[(1r,4S)-4-(pyrrolidin-1-yl)cyclohexyl]ethan-1-one × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;293 K;10% PEG 8000 25% Glycerol 0.16 M Calcium Acetate 0.08 M Cacodilate pH 6.25 Resolution 2.46 Å R-free 0.341

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.

13 other PDB entries and 22 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DPP9_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–863; UniProt 1–863 Author chain B; PDBConstruct 1–863; UniProt 1–863 Author chain C; PDBConstruct 1–863; UniProt 1–863 Author chain D; PDBConstruct 1–863; UniProt 1–863

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 7svl

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7svl
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7svl
Deposition date deposition_date2021-11-19
Structure title titleDPP9 IN COMPLEX WITH LIGAND ICeD-2
Keywords keywordsDIPEPTIDYL PEPTIDASE, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier56.41
Radius of gyration Rg (electron density) rg_electron56.36
Forward intensity I(0) i01973300000.00
Molecular weight molecular_weight380430.0 kDa
Excluded volume excluded_volume477640 ų
Envelope volume envelope_volume667580 ų
Hydration-shell volume shell_volume95037 ų
Envelope diameter envelope_diameter184.5
Shell Rg shell_rg63.35
Envelope Rg envelope_rg54.55
Shape Rg shape_rg56.36
Total Rg total_rg56.54
Total atoms total_atoms26910
Residues n_residues3307
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 dmax190.8
Rg (real space) rg_real56.33
Rg uncertainty (real space) rg_real_error2.09
I(0) (real space) i0_real1.9730e+09
I(0) uncertainty (real space) i0_real_error4.0290e+07
Rg (reciprocal space) rg_reciprocal56.44
I(0) (reciprocal space) i0_reciprocal1974000000.0000
Solution quality estimate total_estimate0.8856
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary81.8
Skewness Skewness skewness0.167
Kurtosis Kurtosis kurtosis-0.705
Angular range angular_range— – 0.1400 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha704000000.0000
Real-space data points n_real_points29
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.866; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.917

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id7svlA01
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_id7svlA02
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_id7svlB01
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_id7svlB02
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_id7svlC01
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_id7svlC02
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_id7svlD01
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_id7svlD02
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)