5hi4

Binding site elucidation and structure guided design of macrocyclic IL-17A antagonists

Method: X-RAY DIFFRACTION Dmax: 160.2 Å Quality: SUSPICIOUS

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

Interleukin-17A

Homo sapiens

UniProt Q16552

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 heterocomplex Heteromer Protein × 7 PDB declaration: heptameric(7) Consistent with protein copy count Chain A; UniProt 24–155 Chain B; UniProt 24–155 Fragment:UNP residues 24-155 CAT-2000 FAB heavy chain × 2 CAT-2000 FAB light chain × 2 synthetic IL-17A peptide inhibitor × 1 63P (9'S,17'R)-6'-chloro-N-methyl-9'-{[(1-methyl-1H-pyrazol-5-yl)carbonyl]amino}-10',19'-dioxo-2'-oxa-11',18'-diazaspiro[cyclopentane-1,21'-tetracyclo[20.2.2.2~12,15~.1~3,7~]nonacosane]-1'(24'),3'(29'),4',6',12',14',22',25',27'-nonaene-17'-carboxamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 4.5;293 K;10% 2-propanol, 20-24% PEG 6K, 0.1 M sodium acetate pH=4.0-5.0 Resolution 1.80 Å R-free 0.224

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.

43 other PDB entries and 56 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name IL17_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–132; UniProt 24–155 Author chain B; PDBConstruct 1–132; UniProt 24–155

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 5hi4

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5hi4
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5hi4
Deposition date deposition_date2016-01-11
Structure title titleBinding site elucidation and structure guided design of macrocyclic IL-17A antagonists
Keywords keywordsIL-17A, psoriasis, MD simulation, sulfonyl fluoride, inhibitor, macrocycle, IMMUNE SYSTEM-INHIBITOR complex; IMMUNE SYSTEM/INHIBITOR
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier44.03
Radius of gyration Rg (electron density) rg_electron45.32
Forward intensity I(0) i0205603000.00
Molecular weight molecular_weight114680.0 kDa
Excluded volume excluded_volume142600 ų
Envelope volume envelope_volume198440 ų
Hydration-shell volume shell_volume41343 ų
Envelope diameter envelope_diameter173.1
Shell Rg shell_rg42.12
Envelope Rg envelope_rg45.84
Shape Rg shape_rg45.28
Total Rg total_rg45.27
Total atoms total_atoms8113
Residues n_residues1042
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 dmax160.2
Rg (real space) rg_real44.82
Rg uncertainty (real space) rg_real_error1.89
I(0) (real space) i0_real2.0560e+08
I(0) uncertainty (real space) i0_real_error3.9850e+06
Rg (reciprocal space) rg_reciprocal44.04
I(0) (reciprocal space) i0_reciprocal205400000.0000
Solution quality estimate total_estimate0.4993
Solution quality rating solution_quality SUSPICIOUS a SUSPICIOUS solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary35.6
Skewness Skewness skewness0.706
Kurtosis Kurtosis kurtosis-0.031
Angular range angular_range— – 0.1800 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha15510000.0000
Real-space data points n_real_points37
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.544; Stabil: 1.000; Sysdev: 0.032; Positv: 1.000; Valcen: 0.395; Smooth: 0.361

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

Domain ID domain_id5hi4A00
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology90 — Cystine Knot Cytokines, subunit B
Homologous superfamily homologous superfamily10 — Cystine-knot cytokines
Domain ID domain_id5hi4B00
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology90 — Cystine Knot Cytokines, subunit B
Homologous superfamily homologous superfamily10 — Cystine-knot cytokines
Domain ID domain_id5hi4C01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5hi4C02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5hi4D01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5hi4D02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5hi4H01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5hi4H02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5hi4L01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5hi4L02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)